1
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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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2
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Vancraenenbroeck R, Hofmann H. Electrostatics and hydrophobicity in the dynamics of intrinsically disordered proteins. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:133. [PMID: 38127117 PMCID: PMC10739388 DOI: 10.1140/epje/s10189-023-00383-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023]
Abstract
Internal friction is a major contribution to the dynamics of intrinsically disordered proteins (IDPs). Yet, the molecular origin of internal friction has so far been elusive. Here, we investigate whether attractive electrostatic interactions in IDPs modulate internal friction differently than the hydrophobic effect. To this end, we used nanosecond fluorescence correlation spectroscopy (nsFCS) and single-molecule Förster resonance energy transfer (FRET) to quantify the conformation and dynamics of the disordered DNA-binding domains Myc, Max and Mad at different salt concentrations. We find that internal friction effects are stronger when the chain is compacted by electrostatic attractions compared to the hydrophobic effect. Although the effect is moderate, the results show that the heteropolymeric nature of IDPs is reflected in their dynamics.
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Affiliation(s)
- Renee Vancraenenbroeck
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100, Rehovot, Israel
- Present Address: Department of Structural and Molecular Biology, University College London, Darwin Building, 107 Gower Street, London, WC1E 6BT, UK
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Herzl St. 234, 76100, Rehovot, Israel.
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3
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Abstract
Flexibility in complexes between intrinsically disordered proteins and folded ligands is widespread in nature. However, timescales and spatial amplitudes of such dynamics remained unexplored for most systems. Our results show that the disordered cytoplasmic tail of the cell adhesion protein E-cadherin diffuses across the entire surface of its folded binding partner β-catenin at fast submillisecond timescales. The nanometer amplitude of these motions could allow kinases to access their recognition motifs without requiring a dissociation of the complex. We expect that the rugged energy landscape found in the E-cadherin/β-catenin complex is a defining feature of dynamic and partially disordered protein complexes. Intrinsically disordered proteins often form dynamic complexes with their ligands. Yet, the speed and amplitude of these motions are hidden in classical binding kinetics. Here, we directly measure the dynamics in an exceptionally mobile, high-affinity complex. We show that the disordered tail of the cell adhesion protein E-cadherin dynamically samples a large surface area of the protooncogene β-catenin. Single-molecule experiments and molecular simulations resolve these motions with high resolution in space and time. Contacts break and form within hundreds of microseconds without a dissociation of the complex. The energy landscape of this complex is rugged with many small barriers (3 to 4 kBT) and reconciles specificity, high affinity, and extreme disorder. A few persistent contacts provide specificity, whereas unspecific interactions boost affinity.
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4
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Abstract
The thermal motion of charged proteins causes randomly fluctuating electric fields inside cells. According to the fluctuation-dissipation theorem, there is an additional friction force associated with such fluctuations. However, the impact of these fluctuations on the diffusion and dynamics of proteins in the cytoplasm is unclear. Here, we provide an order-of-magnitude estimate of this effect by treating electric field fluctuations within a generalized Langevin equation model with a time-dependent friction memory kernel. We find that electric friction is generally negligible compared to solvent friction. However, a significant slowdown of protein diffusion and dynamics is expected for biomolecules with high net charges such as intrinsically disordered proteins and RNA. The results show that direct contacts between biomolecules in a cell are not necessarily required to alter their dynamics.
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Affiliation(s)
- Dmitrii E Makarov
- Department of Chemistry and Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hagen Hofmann
- Department of Chemical and Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
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5
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Köhn B, Kovermann M. All atom insights into the impact of crowded environments on protein stability by NMR spectroscopy. Nat Commun 2020; 11:5760. [PMID: 33188202 PMCID: PMC7666220 DOI: 10.1038/s41467-020-19616-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/23/2020] [Indexed: 01/16/2023] Open
Abstract
The high density of macromolecules affecting proteins due to volume exclusion has been discussed in theory but numerous in vivo experiments cannot be sufficiently understood taking only pure entropic stabilization into account. Here, we show that the thermodynamic stability of a beta barrel protein increases equally at all atomic levels comparing crowded environments with dilute conditions by applying multidimensional high-resolution NMR spectroscopy in a systematic manner. Different crowding agents evoke a pure stabilization cooperatively and do not disturb the surface or integrity of the protein fold. The here developed methodology provides a solid base that can be easily expanded to incorporate e.g. binding partners to recognize functional consequences of crowded conditions. Our results are relevant to research projects targeting soluble proteins in vivo as it can be anticipated that their thermodynamic stability increase comparably and has consequently to be taken into account to coherently understand intracellular processes.
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Affiliation(s)
- Birgit Köhn
- Department of Chemistry, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany.
- Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany.
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6
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Abstract
Structural disorder is widespread in regulatory protein networks. Weak and transient interactions render disordered proteins particularly sensitive to fluctuations in solution conditions such as ion and crowder concentrations. How this sensitivity alters folding coupled binding reactions, however, has not been fully understood. Here, we demonstrate that salt jointly modulates polymer properties and binding affinities of 5 disordered proteins from a transcription factor network. A combination of single-molecule Förster resonance energy transfer experiments, polymer theory, and molecular simulations shows that all 5 proteins expand with increasing ionic strengths due to Debye-Hückel charge screening. Simultaneously, pairwise affinities between the proteins increase by an order of magnitude within physiological salt limits. A quantitative analysis shows that 50% of the affinity increase can be explained by changes in the disordered state. Disordered state properties therefore have a functional relevance even if these states are not directly involved in biological functions. Numerical solutions of coupled binding equilibria with our results show that networks of homologous disordered proteins can function surprisingly robustly in fluctuating cellular environments, despite the sensitivity of its individual proteins.
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7
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Soranno A, Zosel F, Hofmann H. Internal friction in an intrinsically disordered protein-Comparing Rouse-like models with experiments. J Chem Phys 2018; 148:123326. [PMID: 29604877 DOI: 10.1063/1.5009286] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Internal friction is frequently found in protein dynamics. Its molecular origin however is difficult to conceptualize. Even unfolded and intrinsically disordered polypeptide chains exhibit signs of internal friction despite their enormous solvent accessibility. Here, we compare four polymer theories of internal friction with experimental results on the intrinsically disordered protein ACTR (activator of thyroid hormone receptor). Using nanosecond fluorescence correlation spectroscopy combined with single-molecule Förster resonance energy transfer (smFRET), we determine the time scales of the diffusive chain dynamics of ACTR at different solvent viscosities and varying degrees of compaction. Despite pronounced differences between the theories, we find that all models can capture the experimental viscosity-dependence of the chain relaxation time. In contrast, the observed slowdown upon chain collapse of ACTR is not captured by any of the theories and a mechanistic link between chain dimension and internal friction is still missing, implying that the current theories are incomplete. In addition, a discrepancy between early results on homopolymer solutions and recent single-molecule experiments on unfolded and disordered proteins suggests that internal friction is likely to be a composite phenomenon caused by a variety of processes.
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Affiliation(s)
- Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, USA
| | - Franziska Zosel
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Hagen Hofmann
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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8
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Tedeschi G, Salladini E, Santambrogio C, Grandori R, Longhi S, Brocca S. Conformational response to charge clustering in synthetic intrinsically disordered proteins. Biochim Biophys Acta Gen Subj 2018; 1862:2204-2214. [PMID: 30025858 DOI: 10.1016/j.bbagen.2018.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/05/2018] [Accepted: 07/12/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND Recent theoretical and computational studies have shown that the charge content and, most importantly, the linear distribution of opposite charges are major determinants of conformational properties of intrinsically disordered proteins (IDPs). Charge segregation in a sequence can be measured through κ, which represents a normalized measure of charge asymmetry. A strong inverse correlation between κ and radius of gyration has been previously demonstrated for two independent sets of permutated IDP sequences. METHODS We used two well-characterized IDPs, namely measles virus NTAIL and Hendra virus PNT4, sharing a very similar fraction of charged residues and net charge per residue, but differing in proline (Pro) content. For each protein, we have rationally designed a low- and a high-κ variant endowed with the highest and the lowest κ values compatible with their natural amino acid composition. Then, the conformational properties of wild-type and κ-variants have been assessed by biochemical and biophysical techniques. RESULTS We confirmed a direct correlation between κ and protein compaction. The analysis of our original data along with those available from the literature suggests that Pro content may affects the responsiveness to charge clustering. CONCLUSIONS Charge clustering promotes IDP compaction, but the extent of its effects depends on the sequence context. Proline residues seem to play a role contrasting compaction. GENERAL SIGNIFICANCE These results contribute to the identification of sequence determinants of IDP conformational properties. They may also serve as an asset for rational design of non-natural IDPs with tunable degree of compactness.
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Affiliation(s)
- Giulia Tedeschi
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Edoardo Salladini
- CNRS, Aix Marseille Univ, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille 13288, France
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Sonia Longhi
- CNRS, Aix Marseille Univ, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille 13288, France.
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy.
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9
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Li M, Sun T, Jin F, Yu D, Liu Z. Dimension conversion and scaling of disordered protein chains. MOLECULAR BIOSYSTEMS 2017; 12:2932-40. [PMID: 27440558 DOI: 10.1039/c6mb00415f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To extract protein dimension and energetics information from single-molecule fluorescence resonance energy transfer spectroscopy (smFRET) data, it is essential to establish the relationship between the distributions of the radius of gyration (Rg) and the end-to-end (donor-to-acceptor) distance (Ree). Here, we performed a coarse-grained molecular dynamics simulation to obtain a conformational ensemble of denatured proteins and intrinsically disordered proteins. For any disordered chain with fixed length, there is an excellent linear correlation between the average values of Rg and Ree under various solvent conditions, but the relationship deviates from the prediction of a Gaussian chain. A modified conversion formula was proposed to analyze smFRET data. The formula reduces the discrepancy between the results obtained from FRET and small-angle X-ray scattering (SAXS). The scaling law in a coil-globule transition process was examined where a significant finite-size effect was revealed, i.e., the scaling exponent may exceed the theoretical critical boundary [1/3, 3/5] and the prefactor changes notably during the transition. The Sanchez chain model was also tested and it was shown that the mean-field approximation works well for expanded chains.
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Affiliation(s)
- Maodong Li
- Center for Quantitative Biology, Peking University, Beijing 100871, China.
| | - Tanlin Sun
- Center for Quantitative Biology, Peking University, Beijing 100871, China.
| | - Fan Jin
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Daqi Yu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhirong Liu
- Center for Quantitative Biology, Peking University, Beijing 100871, China. and College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
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10
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Hofmann H. Understanding disordered and unfolded proteins using single-molecule FRET and polymer theory. Methods Appl Fluoresc 2016; 4:042003. [DOI: 10.1088/2050-6120/4/4/042003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Schuler B, Soranno A, Hofmann H, Nettels D. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. Annu Rev Biophys 2016; 45:207-31. [PMID: 27145874 DOI: 10.1146/annurev-biophys-062215-010915] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Andrea Soranno
- 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;
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12
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Li M, Liu Z. Dimensions, energetics, and denaturant effects of the protein unstructured state. Protein Sci 2016; 25:734-47. [PMID: 26683260 DOI: 10.1002/pro.2865] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/09/2015] [Accepted: 12/15/2015] [Indexed: 11/09/2022]
Abstract
Determining the energetics of the unfolded state of a protein is essential for understanding the folding mechanics of ordered proteins and the structure-function relation of intrinsically disordered proteins. Here, we adopt a coil-globule transition theory to develop a general scheme to extract interaction and free energy information from single-molecule fluorescence resonance energy transfer spectroscopy. By combining protein stability data, we have determined the free energy difference between the native state and the maximally collapsed denatured state in a number of systems, providing insight on the specific/nonspecific interactions in protein folding. Both the transfer and binding models of the denaturant effects are demonstrated to account for the revealed linear dependence of inter-residue interactions on the denaturant concentration, and are thus compatible under the coil-globule transition theory to further determine the dimension and free energy of the conformational ensemble of the unfolded state. The scaling behaviors and the effective θ-state are also discussed.
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Affiliation(s)
- Maodong Li
- College of Chemistry and Molecular Engineering, Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
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13
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Naganathan AN, Sanchez-Ruiz JM, Munshi S, Suresh S. Are Protein Folding Intermediates the Evolutionary Consequence of Functional Constraints? J Phys Chem B 2015; 119:1323-33. [DOI: 10.1021/jp510342m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica,
Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Sneha Munshi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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14
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Norouzy A, Assaf KI, Zhang S, Jacob MH, Nau WM. Coulomb Repulsion in Short Polypeptides. J Phys Chem B 2014; 119:33-43. [DOI: 10.1021/jp508263a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Amir Norouzy
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Khaleel I. Assaf
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Shuai Zhang
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Maik H. Jacob
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Werner M. Nau
- Department of Life Sciences
and Chemistry, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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15
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Liu L, Werner M, Gershenson A. Collapse of a long axis: single-molecule Förster resonance energy transfer and serpin equilibrium unfolding. Biochemistry 2014; 53:2903-14. [PMID: 24749911 PMCID: PMC4020580 DOI: 10.1021/bi401622n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/17/2014] [Indexed: 01/25/2023]
Abstract
The energy required for mechanical inhibition of target proteases is stored in the native structure of inhibitory serpins and accessed by serpin structural remodeling. The overall serpin fold is ellipsoidal with one long and two short axes. Most of the structural remodeling required for function occurs along the long axis, while expansion of the short axes is associated with misfolded, inactive forms. This suggests that ellipticity, as typified by the long axis, may be important for both function and folding. Placement of donor and acceptor fluorophores approximately along the long axis or one of the short axes allows single-pair Förster resonance energy transfer (spFRET) to report on both unfolding transitions and the time-averaged shape of different conformations. Equilibrium unfolding and refolding studies of the well-characterized inhibitory serpin α1-antitrypsin reveal that the long axis collapses in the folding intermediates while the monitored short axis expands. These energetically distinct intermediates are thus more spherical than the native state. Our spFRET studies agree with other equilibrium unfolding studies that found that the region around one of the β strands, s5A, which helps define the long axis and must move for functionally required loop insertion, unfolds at low denaturant concentrations. This supports a connection between functionally important structural lability and unfolding in the inhibitory serpins.
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Affiliation(s)
- Lu Liu
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Michael Werner
- Department
of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Anne Gershenson
- Department
of Biochemistry and Molecular Biology, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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16
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Hofmann H, Nettels D, Schuler B. Single-molecule spectroscopy of the unexpected collapse of an unfolded protein at low pH. J Chem Phys 2014; 139:121930. [PMID: 24089742 DOI: 10.1063/1.4820490] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dimensions of intrinsically disordered and unfolded proteins critically depend on the solution conditions, such as temperature, pH, ionic strength, and osmolyte or denarurant concentration. However, a quantitative understanding of how the complex combination of chain-chain and chain-solvent interactions is affected by the solvent is still missing. Here, we take a step towards this goal by investigating the combined effect of pH and denaturants on the dimensions of an unfolded protein. We use single-molecule fluorescence spectroscopy to extract the dimensions of unfolded cold shock protein (CspTm) in mixtures of the denaturants urea and guanidinium chloride (GdmCl) at neutral and acidic pH. Surprisingly, even though a change in pH from 7 to 2.9 increases the net charge of CspTm from -3.8 to +10.2, the radius of gyration of the chain is very similar under both conditions, indicating that protonation of acidic side chains at low pH results in additional hydrophobic interactions. We use a simple shared binding site model that describes the joint effect of urea and GdmCl, together with polyampholyte theory and an ion cloud model that includes the chemical free energy of counterion interactions and side chain protonation, to quantify this effect.
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Affiliation(s)
- Hagen Hofmann
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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17
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Brucale M, Schuler B, Samorì B. Single-molecule studies of intrinsically disordered proteins. Chem Rev 2014; 114:3281-317. [PMID: 24432838 DOI: 10.1021/cr400297g] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marco Brucale
- Institute for the Study of Nanostructured Materials (ISMN), Italian National Council of Research (CNR) , Area della Ricerca Roma1, Via Salaria km 29.3 00015 Monterotondo (Rome), Italy
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18
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Udgaonkar JB. Polypeptide chain collapse and protein folding. Arch Biochem Biophys 2013; 531:24-33. [DOI: 10.1016/j.abb.2012.10.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/01/2012] [Accepted: 10/08/2012] [Indexed: 12/11/2022]
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19
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Schuler B, Hofmann H. Single-molecule spectroscopy of protein folding dynamics—expanding scope and timescales. Curr Opin Struct Biol 2013; 23:36-47. [DOI: 10.1016/j.sbi.2012.10.008] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
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20
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Hirschfeld V, Paulsen H, Hübner CG. The spectroscopic ruler revisited at 77 K. Phys Chem Chem Phys 2013; 15:17664-71. [DOI: 10.1039/c3cp51106e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Voelz VA, Jäger M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS. Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. J Am Chem Soc 2012; 134:12565-77. [PMID: 22747188 DOI: 10.1021/ja302528z] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein folding is a fundamental process in biology, key to understanding many human diseases. Experimentally, proteins often appear to fold via simple two- or three-state mechanisms involving mainly native-state interactions, yet recent network models built from atomistic simulations of small proteins suggest the existence of many possible metastable states and folding pathways. We reconcile these two pictures in a combined experimental and simulation study of acyl-coenzyme A binding protein (ACBP), a two-state folder (folding time ~10 ms) exhibiting residual unfolded-state structure, and a putative early folding intermediate. Using single-molecule FRET in conjunction with side-chain mutagenesis, we first demonstrate that the denatured state of ACBP at near-zero denaturant is unusually compact and enriched in long-range structure that can be perturbed by discrete hydrophobic core mutations. We then employ ultrafast laminar-flow mixing experiments to study the folding kinetics of ACBP on the microsecond time scale. These studies, along with Trp-Cys quenching measurements of unfolded-state dynamics, suggest that unfolded-state structure forms on a surprisingly slow (~100 μs) time scale, and that sequence mutations strikingly perturb both time-resolved and equilibrium smFRET measurements in a similar way. A Markov state model (MSM) of the ACBP folding reaction, constructed from over 30 ms of molecular dynamics trajectory data, predicts a complex network of metastable stables, residual unfolded-state structure, and kinetics consistent with experiment but no well-defined intermediate preceding the main folding barrier. Taken together, these experimental and simulation results suggest that the previously characterized fast kinetic phase is not due to formation of a barrier-limited intermediate but rather to a more heterogeneous and slow acquisition of unfolded-state structure.
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Affiliation(s)
- Vincent A Voelz
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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22
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Pashley CL, Morgan GJ, Kalverda AP, Thompson GS, Kleanthous C, Radford SE. Conformational properties of the unfolded state of Im7 in nondenaturing conditions. J Mol Biol 2012; 416:300-18. [PMID: 22226836 PMCID: PMC3314952 DOI: 10.1016/j.jmb.2011.12.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 11/04/2022]
Abstract
The unfolded ensemble in aqueous solution represents the starting point of protein folding. Characterisation of this species is often difficult since the native state is usually predominantly populated at equilibrium. Previous work has shown that the four-helix protein, Im7 (immunity protein 7), folds via an on-pathway intermediate. While the transition states and folding intermediate have been characterised in atomistic detail, knowledge of the unfolded ensemble under the same ambient conditions remained sparse. Here, we introduce destabilising amino acid substitutions into the sequence of Im7, such that the unfolded state becomes predominantly populated at equilibrium in the absence of denaturant. Using far- and near-UV CD, fluorescence, urea titration and heteronuclear NMR experiments, we show that three amino acid substitutions (L18A-L19A-L37A) are sufficient to prevent Im7 folding, such that the unfolded state is predominantly populated at equilibrium. Using measurement of chemical shifts, (15)N transverse relaxation rates and sedimentation coefficients, we show that the unfolded species of L18A-L19A-L37A deviates significantly from random-coil behaviour. Specifically, we demonstrate that this unfolded species is compact (R(h)=25 Å) relative to the urea-denatured state (R(h)≥30 Å) and contains local clusters of hydrophobic residues in regions that correspond to the four helices in the native state. Despite these interactions, there is no evidence for long-range stabilising tertiary interactions or persistent helical structure. The results reveal an unfolded ensemble that is conformationally restricted in regions of the polypeptide chain that ultimately form helices I, II and IV in the native state.
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Key Words
- ts1, transition state 1
- ts2, transition state 2
- cole7, colicin e7
- ssp, secondary structure propensity
- smfret, single-molecule förster resonance energy transfer
- im7, immunity protein 7
- edta, ethylenediaminetetraacetic acid
- hsqc, heteronuclear single quantum coherence
- auc, analytical ultracentrifugation
- itc, isothermal titration calorimetry
- bmrb, biological magnetic resonance data bank
- noe, nuclear overhauser enhancement
- aabuf, average area buried upon folding
- pdb, protein data bank
- protein folding
- nmr
- unfolded ensemble
- denatured state
- immunity protein
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Affiliation(s)
- Clare L. Pashley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Gareth J. Morgan
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Arnout P. Kalverda
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Gary S. Thompson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
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23
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Haran G. How, when and why proteins collapse: the relation to folding. Curr Opin Struct Biol 2011; 22:14-20. [PMID: 22104965 DOI: 10.1016/j.sbi.2011.10.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 10/15/2011] [Accepted: 10/18/2011] [Indexed: 11/25/2022]
Abstract
Unfolded proteins under strongly denaturing conditions are highly expanded. However, when the conditions are more close to native, an unfolded protein may collapse to a compact globular structure distinct from the folded state. This transition is akin to the coil-globule transition of homopolymers. Single-molecule FRET experiments have been particularly conducive in revealing the collapsed state under conditions of coexistence with the folded state. The collapse can be even more readily observed in natively unfolded proteins. Time-resolved studies, using FRET and small-angle scattering, have shown that the collapse transition is a very fast event, probably occurring on the submicrosecond time scale. The forces driving collapse are likely to involve both hydrophobic and backbone interactions. The loss of configurational entropy during collapse makes the unfolded state less stable compared to the folded state, thus facilitating folding.
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Affiliation(s)
- Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, Rehovot 76100, Israel
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24
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England JL, Haran G. Role of solvation effects in protein denaturation: from thermodynamics to single molecules and back. Annu Rev Phys Chem 2011; 62:257-77. [PMID: 21219136 DOI: 10.1146/annurev-physchem-032210-103531] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein stability often is studied in vitro through the use of urea and guanidinium chloride, chemical cosolvents that disrupt protein native structure. Much controversy still surrounds the underlying mechanism by which these molecules denature proteins. Here we review current thinking on various aspects of chemical denaturation. We begin by discussing classic models of protein folding and how the effects of denaturants may fit into this picture through their modulation of the collapse, or coil-globule transition, which typically precedes folding. Subsequently, we examine recent molecular dynamics simulations that have shed new light on the possible microscopic origins of the solvation effects brought on by denaturants. It seems likely that both denaturants operate by facilitating solvation of hydrophobic regions of proteins. Finally, we present recent single-molecule fluorescence studies of denatured proteins, the analysis of which corroborates the role of denaturants in shifting the equilibrium of the coil-globule transition.
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Affiliation(s)
- Jeremy L England
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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25
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Rosenkranz T, Schlesinger R, Gabba M, Fitter J. Native and Unfolded States of Phosphoglycerate Kinase Studied by Single‐Molecule FRET. Chemphyschem 2010; 12:704-10. [DOI: 10.1002/cphc.201000701] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 09/29/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Tobias Rosenkranz
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Ramona Schlesinger
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Matteo Gabba
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
| | - Jörg Fitter
- Research Centre Jülich, ISB‐2: Molecular Biophysics, 52425 Jülich (Germany), Fax: (+49) 2461 61 1448
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26
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Hirschfeld V, Hübner CG. A sensitive and versatile laser scanning confocal optical microscope for single-molecule fluorescence at 77 K. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:113705. [PMID: 21133476 DOI: 10.1063/1.3499260] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We developed a cryostat suitable for a laser scanning confocal microscope which allows for a short working distance and thus the usage of an objective with a high numerical aperture ensuring high collection efficiency. The in situ preparation of a thin layer of amorphous water is realized in a part of the cryostat, a Dewar vessel, which is put onto a custom-made, liquid-nitrogen immersed spin-coater. First tests on the setup are performed on a perylenemonoimide/polymethyl methacrylate model system using a standard oil objective and a dry objective at ambient temperature as well as a dry objective at liquid nitrogen temperature (77 K). Fluorescence resonance energy transfer (FRET) measurements on doubly labeled, freeze-quenched polyproline chains show the applicability of the new method on biomolecules. The alternating laser excitation (ALEX) is modified to a line-scanning process (slow ALEX) to optimize the sorting of the labeled molecules. Photophysics and photochemistry at liquid nitrogen temperature are investigated.
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Affiliation(s)
- V Hirschfeld
- Institute of Physics, University of Lübeck, Ratzeburger Allee 160, Lübeck, Germany
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27
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Dasgupta A, Udgaonkar JB. Evidence for initial non-specific polypeptide chain collapse during the refolding of the SH3 domain of PI3 kinase. J Mol Biol 2010; 403:430-45. [PMID: 20837026 DOI: 10.1016/j.jmb.2010.08.046] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 08/22/2010] [Accepted: 08/24/2010] [Indexed: 12/01/2022]
Abstract
Refolding of the SH3 domain of PI3 kinase from the guanidine hydrochloride (GdnHCl)-unfolded state has been probed with millisecond (stopped flow) and sub-millisecond (continuous flow) measurements of the change in fluorescence, circular dichroism, ANS fluorescence and three-site fluorescence resonance energy transfer (FRET) efficiency. Fluorescence measurements are unable to detect structural changes preceding the rate-limiting step of folding, whereas measurements of changes in ANS fluorescence and FRET efficiency indicate that polypeptide chain collapse precedes the major structural transition. The initial chain collapse reaction is complete within 150 μs. The collapsed form at this time possesses hydrophobic clusters to which ANS binds. Each of the three measured intra-molecular distances has contracted to an extent predicted by the dependence of the FRET signal in completely unfolded protein on denaturant concentration, indicating that contraction is non-specific. The extent of contraction of each intra-molecular distance in the collapsed product of sub-millisecond folding increases continuously with a decrease in [GdnHCl]. The gradual contraction is continuous with the gradual contraction seen in completely unfolded protein, and its dependence on [GdnHCl] is not indicative of an all-or-none collapse reaction. The dependence of the extent of contraction on [GdnHCl] was similar for the three distances, indicating that chain collapse occurs in a synchronous manner across different segments of the polypeptide chain. The sub-millisecond measurements of folding in GdnHCl were unable to determine whether hydrophobic cluster formation, probed by ANS fluorescence measurement, precedes chain contraction probed by FRET. To determine whether hydrogen bonding plays a role in initial chain collapse, folding was initiated by dilution of the urea-unfolded state. The extent of contraction of at least one intra-molecular distance in the collapsed product of sub-millisecond folding in urea is similar to that seen in GdnHCl, and the initial contraction in urea too appears to be gradual.
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Affiliation(s)
- Amrita Dasgupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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28
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Ziv G, Haran G. Protein folding, protein collapse, and tanford's transfer model: lessons from single-molecule FRET. J Am Chem Soc 2010; 131:2942-7. [PMID: 19239269 DOI: 10.1021/ja808305u] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The essential and nontrivial role of the denatured state of proteins in their folding reaction is being increasingly scrutinized in recent years. Single molecule FRET (smFRET) experiments show that the denatured state undergoes a continuous collapse (or coil-to-globule) transition as the concentration of a chemical denaturant is decreased, suggesting that conformational entropy of the denatured state is an important part of the free energy of folding. Such observations question the validity of the classical Tanford transfer model, which suggests that the folding free energy can be understood solely based on the difference in amino acid solvation between the folded state and a fixed unfolded state. An alternative to the transfer model is obtained here from a polymer theoretical analysis of a series of published smFRET data. The analysis shows that the free energy of denatured-state collapse has a linear dependence on denaturant concentration, an outcome of the interplay between enthalpic and entropic contributions. Surprisingly, the slope of the free energy of collapse agrees very well with the respective slope of the free energy of folding. This conformity of values obtained from two very different measurements shows that it is the collapse transition in the denatured state which mediates the effect of denaturants on folding. The energetics of folding are thus governed by the competition of solvation and conformational entropy in the denatured state.
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Affiliation(s)
- Guy Ziv
- Chemical Physics Department, Weizmann Institute of Science, Rehovot 76100, Israel
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29
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From the Cover: Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci U S A 2010; 107:14609-14. [PMID: 20639465 DOI: 10.1073/pnas.1001743107] [Citation(s) in RCA: 411] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Many eukaryotic proteins are disordered under physiological conditions, and fold into ordered structures only on binding to their cellular targets. Such intrinsically disordered proteins (IDPs) often contain a large fraction of charged amino acids. Here, we use single-molecule Förster resonance energy transfer to investigate the influence of charged residues on the dimensions of unfolded and intrinsically disordered proteins. We find that, in contrast to the compact unfolded conformations that have been observed for many proteins at low denaturant concentration, IDPs can exhibit a prominent expansion at low ionic strength that correlates with their net charge. Charge-balanced polypeptides, however, can exhibit an additional collapse at low ionic strength, as predicted by polyampholyte theory from the attraction between opposite charges in the chain. The pronounced effect of charges on the dimensions of unfolded proteins has important implications for the cellular functions of IDPs.
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30
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Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. Proc Natl Acad Sci U S A 2009; 106:20740-5. [PMID: 19933333 DOI: 10.1073/pnas.0900622106] [Citation(s) in RCA: 189] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used single-molecule FRET in combination with other biophysical methods and molecular simulations to investigate the effect of temperature on the dimensions of unfolded proteins. With single-molecule FRET, this question can be addressed even under near-native conditions, where most molecules are folded, allowing us to probe a wide range of denaturant concentrations and temperatures. We find a compaction of the unfolded state of a small cold shock protein with increasing temperature in both the presence and the absence of denaturant, with good agreement between the results from single-molecule FRET and dynamic light scattering. Although dissociation of denaturant from the polypeptide chain with increasing temperature accounts for part of the compaction, the results indicate an important role for additional temperature-dependent interactions within the unfolded chain. The observation of a collapse of a similar extent in the extremely hydrophilic, intrinsically disordered protein prothymosin alpha suggests that the hydrophobic effect is not the sole source of the underlying interactions. Circular dichroism spectroscopy and replica exchange molecular dynamics simulations in explicit water show changes in secondary structure content with increasing temperature and suggest a contribution of intramolecular hydrogen bonding to unfolded state collapse.
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31
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Liu P, Meng X, Qu P, Zhao XS, Wang CC. Subdomain-Specific Collapse of Denatured Staphylococcal Nuclease Revealed by Single Molecule Fluorescence Resonance Energy Transfer Measurements. J Phys Chem B 2009; 113:12030-6. [PMID: 19678648 DOI: 10.1021/jp809825x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pengcheng Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xianglan Meng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peng Qu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin Sheng Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chih-chen Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China, Graduate School of the Chinese Academy of Sciences, Beijing 100049, China, Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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32
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Hofmann H, Weininger U, Löw C, Golbik RP, Balbach J, Ulbrich-Hofmann R. Fast amide proton exchange reveals close relation between native-state dynamics and unfolding kinetics. J Am Chem Soc 2009; 131:140-6. [PMID: 19061322 DOI: 10.1021/ja8048942] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
It has long been recognized that many proteins fold and unfold via partially structured intermediates, but it is still unclear why some proteins unfold in a two-state fashion while others do not. Here we compare the unfolding pathway of the small one-domain protein barstar with its dynamics under native conditions. Using very fast proton-exchange experiments, extensive dynamic heterogeneity within the native-state ensemble could be identified. Especially the dynamics of helix 3, covering the hydrophobic core of the molecule, is found to be clearly cooperative but decoupled from the global dynamics. Moreover, an initial unfolding of this helix followed by the breakdown of the remaining tertiary structure can be concluded from the comparison of the proton exchange experiments with unfolding kinetics detected by stopped-flow fluorescence. We infer that the unfolding pathway of barstar is closely coupled to its native-state dynamics.
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Affiliation(s)
- Hagen Hofmann
- Institute of Biochemistry and Biotechnology, Institute of Physics, Biophysics group and Mitteldeutsches Zentrum für Struktur and Dynamik der Proteine (MZP), Martin-Luther University Halle-Wittenberg, 06099 Halle
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33
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Orevi T, Ben Ishay E, Pirchi M, Jacob MH, Amir D, Haas E. Early closure of a long loop in the refolding of adenylate kinase: a possible key role of non-local interactions in the initial folding steps. J Mol Biol 2008; 385:1230-42. [PMID: 19013178 DOI: 10.1016/j.jmb.2008.10.077] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2008] [Revised: 09/16/2008] [Accepted: 10/27/2008] [Indexed: 11/25/2022]
Abstract
Most globular protein chains, when transferred from high to low denaturant concentrations, collapse instantly before they refold to their native state. The initial compaction of the protein molecule is assumed to have a key effect on the folding pathway, but it is not known whether the earliest structures formed during or instantly after collapse are defined by local or by non-local interactions--that is, by secondary structural elements or by loop closure of long segments of the protein chain. Stable closure of one or several long loops can reduce the chain entropy at a very early stage and can prevent the protein from following non-productive pathways whose number grows exponentially with the length of the protein chain. In Escherichia coli adenylate kinase (AK), about seven long loops define the topology of the native structure. We selected four loop-forming sections of the chain and probed the time course of loop formation during refolding of AK. We labeled the termini of the loop segments with tryptophan and cysteine-5-amidosalicylic acid. This donor-acceptor pair of probes used with fluorescence resonance excitation energy transfer spectroscopy (FRET) is suitable for detecting very short distances and thus is able to distinguish between random and specific compactions. Refolding of AK was initiated by stopped-flow mixing, followed simultaneously by donor and acceptor fluorescence, and analyzed in terms of energy transfer efficiency and distance. In the collapsed state of AK, observed after the 5-ms dead time of the instrument, one of the selected segments shows a native-like separation of its termini; it forms a loop already in the collapsed state. A second segment that includes the first but is longer by 15 residues shows an almost native-like separation of its termini. In contrast, a segment that is shorter but part of the second segment shows a distance separation of its termini as high as a segment that spans almost the whole protein chain. We conclude that a specific network of non-local interactions, the closure of one or several loops, can play an important role in determining the protein folding pathway at its early phases.
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Affiliation(s)
- Tomer Orevi
- The E. Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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34
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Guo L, Chowdhury P, Glasscock JM, Gai F. Denaturant-induced expansion and compaction of a multi-domain protein: IgG. J Mol Biol 2008; 384:1029-36. [PMID: 19004457 DOI: 10.1016/j.jmb.2008.03.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 02/26/2008] [Accepted: 03/05/2008] [Indexed: 10/22/2022]
Abstract
It is generally believed that unfolded or denatured proteins show random-coil statistics and hence their radius of gyration simply scales with solvent quality (or concentration of denaturant). Indeed, nearly all proteins studied thus far have been shown to undergo a gradual and continuous expansion with increasing concentration of denaturant. Here, we use fluorescence correlation spectroscopy (FCS) to show that while protein A, a multi-domain and predominantly helical protein, expands gradually and continuously with increasing concentration of guanidine hydrochloride (GdnHCl), the F(ab')2 fragment of goat anti-rabbit antibody IgG, a multi-subunit all beta-sheet protein does not show such continuous expansion behavior. Instead, it first expands and then contracts with increasing concentration of GdnHCl. Even more striking is the fact that the hydrodynamic radius of the most expanded F(ab')2 ensemble, observed at 3-4 M GdnHCl, is approximately 3.6 times that of the native protein. Further FCS measurements involving urea and NaCl show that the unusually expanded F(ab')2 conformations might be due to electrostatic repulsions. Taken together, these results suggest that specific interactions need to be considered while assessing the conformational and statistical properties of unfolded proteins, particularly under conditions of low solvent quality.
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Affiliation(s)
- Lin Guo
- Department of Chemistry, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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