1
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Kaynak BT, Dahmani ZL, Doruker P, Banerjee A, Yang SH, Gordon R, Itzhaki LS, Bahar I. Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A. Structure 2023; 31:607-618.e3. [PMID: 36948205 PMCID: PMC10164121 DOI: 10.1016/j.str.2023.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/25/2023] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
PR65, a horseshoe-shaped scaffold composed of 15 HEAT (observed in Huntingtin, elongation factor 3, protein phosphatase 2A, and the yeast kinase TOR1) repeats, forms, together with catalytic and regulatory subunits, the heterotrimeric protein phosphatase PP2A. We examined the role of PR65 in enabling PP2A enzymatic activity with computations at various levels of complexity, including hybrid approaches that combine full-atomic and elastic network models. Our study points to the high flexibility of this scaffold allowing for end-to-end distance fluctuations of 40-50 Å between compact and extended conformations. Notably, the intrinsic dynamics of PR65 facilitates complexation with the catalytic subunit and is retained in the PP2A complex enabling PR65 to engage the two domains of the catalytic subunit and provide the mechanical framework for enzymatic activity, with support from the regulatory subunit. In particular, the intra-repeat coils at the C-terminal arm play an important role in allosterically mediating the collective dynamics of PP2A, pointing to target sites for modulating PR65 function.
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Affiliation(s)
- Burak T Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Zakaria L Dahmani
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Shang-Hua Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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2
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Wang Z, Wang M, Zhao Z, Zheng P. Quantification of carboxylate-bridged di-zinc site stability in protein due ferri by single-molecule force spectroscopy. Protein Sci 2023; 32:e4583. [PMID: 36718829 PMCID: PMC9926469 DOI: 10.1002/pro.4583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/16/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Carboxylate-bridged diiron proteins belong to a protein family involved in different physiological processes. These proteins share the conservative EXXH motif, which provides the carboxylate bridge and is critical for metal binding. Here, we choose de novo-designed single-chain due ferri protein (DFsc), a four-helical protein with two EXXH motifs as a model protein, to study the stability of the carboxylate-bridged di-metal binding site. The mechanical and kinetic properties of the di-Zn site in DFsc were obtained by atomic force microscopy-based single-molecule force spectroscopy. Zn-DFsc showed a considerable rupture force of ~200 pN, while the apo-protein is mechanically labile. In addition, multiple rupture pathways were observed with different probabilities, indicating the importance of the EXXH-based carboxylate-bridged metal site. These results demonstrate carboxylate-bridged di-metal site is mechanically stable and improve our understanding of this important type of metalloprotein.
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Affiliation(s)
- Zhiyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Mengdie Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Zhongxin Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
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3
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Medur Gurushankar MS, Dalvi S, Venkatraman P. Snapshots of urea-induced early structural changes and unfolding of an ankyrin repeat protein at atomic resolution. Protein Sci 2022; 31:e4515. [PMID: 36382986 PMCID: PMC9703593 DOI: 10.1002/pro.4515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022]
Abstract
Protein folding and unfolding is a complex process, underscored by the many proteotoxic diseases associated with misfolded proteins. Mapping pathways from a native structure to an unfolded protein or vice versa, identifying the intermediates, and defining the role of sequence and structure en route remain outstanding problems in the field. It is even more challenging to capture the events at atomistic resolution. X-ray diffraction has so far been used to understand how urea interacts with and unfolds two stable globular proteins. Here, we present the case study on PSMD10Gankyrin , a prototype for a moderately stable, non-globular repeat protein, long and rigid, with its termini located at either end. We define structural changes in the time dimension using low urea concentrations to arrive at the following conclusions. (a) Unfolding is rapidly initiated at the C-terminus, slowly at the N-terminus, and proceeds inwards from both ends. (b) C-terminus undergoes an α to 310 helix transition, representing the structure of a potential early unfolding intermediate before disorder sets in. (c) Distinct and progressive changes in the electrostatic landscape of PSMD10Gankyrin were observed, indicative of conformational changes in the seemingly inflexible motif involved in protein-protein interaction. We believe this unique study will open up the field for better and bolder queries and increase the choice of model proteins for a better understanding of the challenging problems of protein folding, protein interactions, protein degradation, and diseases associated with misfolding.
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Affiliation(s)
- Mukund Sudharsan Medur Gurushankar
- Protein Interactome Laboratory for Structural and Functional BiologyAdvanced Centre for Treatment, Research and Education in CancerNavi MumbaiMaharashtraIndia
- Department of Biochemistry and PharmacologyBio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoriaAustralia
| | - Somavally Dalvi
- Protein Interactome Laboratory for Structural and Functional BiologyAdvanced Centre for Treatment, Research and Education in CancerNavi MumbaiMaharashtraIndia
- Department of Biochemistry and PharmacologyBio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoriaAustralia
- Present address:
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneVictoriaAustralia
| | - Prasanna Venkatraman
- Protein Interactome Laboratory for Structural and Functional BiologyAdvanced Centre for Treatment, Research and Education in CancerNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
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4
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Synakewicz M, Eapen RS, Perez-Riba A, Rowling PJE, Bauer D, Weißl A, Fischer G, Hyvönen M, Rief M, Itzhaki LS, Stigler J. Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix. ACS NANO 2022. [PMID: 35258937 DOI: 10.1101/2021.03.27.437344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Tandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs), superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between partially folded and unfolded conformations. We rationalize the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the center toward both termini simultaneously. Most strikingly, we also directly observe the protein's superhelical tertiary structure in the force signal. Using protein engineering, crystallography, and single-molecule experiments, we show that the superhelical geometry can be altered by carefully placed amino acid substitutions, and we examine how these sequence changes affect intrinsic repeat stability and inter-repeat coupling. Our findings provide the means to dissect and modulate repeat-protein stability and dynamics, which will be essential for researchers to understand the function of natural repeat proteins and to exploit artificial repeats proteins in nanotechnology and biomedical applications.
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Affiliation(s)
- Marie Synakewicz
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Rohan S Eapen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Albert Perez-Riba
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Pamela J E Rowling
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Daniela Bauer
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Andreas Weißl
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Matthias Rief
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 München, Germany
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5
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Synakewicz M, Eapen RS, Perez-Riba A, Rowling PJE, Bauer D, Weißl A, Fischer G, Hyvönen M, Rief M, Itzhaki LS, Stigler J. Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix. ACS NANO 2022; 16:3895-3905. [PMID: 35258937 PMCID: PMC8944806 DOI: 10.1021/acsnano.1c09162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Tandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs), superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between partially folded and unfolded conformations. We rationalize the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the center toward both termini simultaneously. Most strikingly, we also directly observe the protein's superhelical tertiary structure in the force signal. Using protein engineering, crystallography, and single-molecule experiments, we show that the superhelical geometry can be altered by carefully placed amino acid substitutions, and we examine how these sequence changes affect intrinsic repeat stability and inter-repeat coupling. Our findings provide the means to dissect and modulate repeat-protein stability and dynamics, which will be essential for researchers to understand the function of natural repeat proteins and to exploit artificial repeats proteins in nanotechnology and biomedical applications.
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Affiliation(s)
- Marie Synakewicz
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Rohan S. Eapen
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Albert Perez-Riba
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Pamela J. E. Rowling
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Daniela Bauer
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Andreas Weißl
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Gerhard Fischer
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Matthias Rief
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Laura S. Itzhaki
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Johannes Stigler
- Gene
Center Munich, Ludwig-Maximilians-Universität
München, Feodor-Lynen-Straße 25, 81377 München, Germany
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6
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Abstract
Abstract
Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein–protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.
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7
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Wang Z, Nie J, Shi S, Li G, Zheng P. Transforming de novo protein α 3D into a mechanically stable protein by zinc binding. Chem Commun (Camb) 2021; 57:11489-11492. [PMID: 34651619 DOI: 10.1039/d1cc04908a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
α3D is a de novo designed three-helix bundle protein. Like most naturally occurring helical proteins, it is mechanically labile with an unfolding force of <15 pN, revealed by atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). This protein has been further designed with a tri-cysteine metal-binding site, named α3DIV, which can bind heavy transition metals. Here, we demonstrate that incorporating such a metal-binding site can transform this mechanically labile protein into a stable one. We show that zinc binds to the tri-cysteine site and increases the unfolding force to ∼160 pN. This force is one order of magnitude higher than that of the apo-protein (<15 pN). Moreover, the unfolding mechanism of Zn-α3DIV indicates the correct zinc binding with the tri-cysteine site, forming three mechanostable Zn-thiolate bonds. Thus, α3DIV could be a potential α-helical structure-based building block for synthesizing biomaterials with tunable mechanical properties.
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Affiliation(s)
- Ziyi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Shengcao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Guoqiang Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
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8
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Díaz-García C, Hornos F, Giudici AM, Cámara-Artigas A, Luque-Ortega JR, Arbe A, Rizzuti B, Alfonso C, Forwood JK, Iovanna JL, Gómez J, Prieto M, Coutinho A, Neira JL. Human importin α3 and its N-terminal truncated form, without the importin-β-binding domain, are oligomeric species with a low conformational stability in solution. Biochim Biophys Acta Gen Subj 2020; 1864:129609. [PMID: 32234409 DOI: 10.1016/j.bbagen.2020.129609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 03/13/2020] [Accepted: 03/26/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Eukaryotic cells have a continuous transit of macromolecules between the cytoplasm and the nucleus. Several carrier proteins are involved in this transport. One of them is importin α, which must form a complex with importin β to accomplish its function, by domain-swapping its 60-residue-long N terminus. There are several human isoforms of importin α; among them, importin α3 has a particularly high flexibility. METHODS We studied the conformational stability of intact importin α3 (Impα3) and its truncated form, where the 64-residue-long, N-terminal importin-β-binding domain (IBB) has been removed (ΔImpα3), in a wide pH range, with several spectroscopic, biophysical, biochemical methods and with molecular dynamics (MD). RESULTS Both species acquired native-like structure between pH 7 and 10.0, where Impα3 was a dimer (with an apparent self-association constant of ~10 μM) and ΔImpα3 had a higher tendency to self-associate than the intact species. The acquisition of secondary, tertiary and quaternary structure, and the burial of hydrophobic patches, occurred concomitantly. Both proteins unfolded irreversibly at physiological pH, by using either temperature or chemical denaturants, through several partially folded intermediates. The MD simulations support the presence of these intermediates. CONCLUSIONS The thermal stability of Impα3 at physiological pH was very low, but was higher than that of ΔImpα3. Both proteins were stable in a narrow pH range, and they unfolded at physiological pH populating several intermediate species. GENERAL SIGNIFICANCE The low conformational stability explains the flexibility of Impα3, which is needed to carry out its recognition of complex cargo sequences.
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Affiliation(s)
- Clara Díaz-García
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Felipe Hornos
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | | | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- ceiA3, 04120 Almería, Spain
| | - Juan Román Luque-Ortega
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU), Materials Physics Center (MPC), 20018 San Sebastián, Spain
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Juan L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, 163 Avenue de Luminy, 13288 Marseille, France
| | - Javier Gómez
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Manuel Prieto
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Ana Coutinho
- iBB- Institute for Bioengineering and Bioscience, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal; Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1649-004 Lisboa, Portugal
| | - José L Neira
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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9
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Perez-Riba A, Komives E, Main ERG, Itzhaki LS. Decoupling a tandem-repeat protein: Impact of multiple loop insertions on a modular scaffold. Sci Rep 2019; 9:15439. [PMID: 31659184 PMCID: PMC6817815 DOI: 10.1038/s41598-019-49905-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/29/2019] [Indexed: 11/25/2022] Open
Abstract
The simple topology and modular architecture of tandem-repeat proteins such as tetratricopeptide repeats (TPRs) and ankyrin repeats makes them straightforward to dissect and redesign. Repeat-protein stability can be manipulated in a predictable way using site-specific mutations. Here we explore a different type of modification - loop insertion - that will enable a simple route to functionalisation of this versatile scaffold. We previously showed that a single loop insertion has a dramatically different effect on stability depending on its location in the repeat array. Here we dissect this effect by a combination of multiple and alternated loop insertions to understand the origins of the context-dependent loss in stability. We find that the scaffold is remarkably robust in that its overall structure is maintained. However, adjacent repeats are now only weakly coupled, and consequently the increase in solvent protection, and thus stability, with increasing repeat number that defines the tandem-repeat protein class is lost. Our results also provide us with a rulebook with which we can apply these principles to the design of artificial repeat proteins with precisely tuned folding landscapes and functional capabilities, thereby paving the way for their exploitation as a versatile and truly modular platform in synthetic biology.
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Affiliation(s)
- Albert Perez-Riba
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | - Elizabeth Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0378, USA
| | - Ewan R G Main
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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10
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Li Q, Scholl ZN, Marszalek PE. Unraveling the Mechanical Unfolding Pathways of a Multidomain Protein: Phosphoglycerate Kinase. Biophys J 2019; 115:46-58. [PMID: 29972811 DOI: 10.1016/j.bpj.2018.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/31/2018] [Accepted: 05/21/2018] [Indexed: 01/12/2023] Open
Abstract
Phosphoglycerate kinase (PGK) is a highly conserved enzyme that is crucial for glycolysis. PGK is a monomeric protein composed of two similar domains and has been the focus of many studies for investigating interdomain interactions within the native state and during folding. Previous studies used traditional biophysical methods (such as circular dichroism, tryptophan fluorescence, and NMR) to measure signals over a large ensemble of molecules, which made it difficult to observe transient changes in stability or structure during unfolding and refolding of single molecules. Here, we unfold single molecules of PGK using atomic force spectroscopy and steered molecular dynamic computer simulations to examine the conformational dynamics of PGK during its unfolding process. Our results show that after the initial forced separation of its domains, yeast PGK (yPGK) does not follow a single mechanical unfolding pathway; instead, it stochastically follows two distinct pathways: unfolding from the N-terminal domain or unfolding from the C-terminal domain. The truncated yPGK N-terminal domain unfolds via a transient intermediate, whereas the structurally similar isolated C-terminal domain has no detectable intermediates throughout its mechanical unfolding process. The N-terminal domain in the full-length yPGK displays a strong unfolding intermediate 13% of the time, whereas the truncated domain (yPGKNT) transitions through the intermediate 81% of the time. This effect indicates that the mechanical properties of yPGK cannot be simply deduced from the mechanical properties of its constituents. We also find that Escherichia coli PGK is significantly less mechanically stable as compared to yPGK, contrary to bulk unfolding measurements. Our results support the growing body of observations that the folding behavior of multidomain proteins is difficult to predict based solely on the studies of isolated domains.
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Affiliation(s)
- Qing Li
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| | - Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| | - Piotr E Marszalek
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
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11
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Perez-Riba A, Lowe AR, Main ERG, Itzhaki LS. Context-Dependent Energetics of Loop Extensions in a Family of Tandem-Repeat Proteins. Biophys J 2019; 114:2552-2562. [PMID: 29874606 PMCID: PMC6129472 DOI: 10.1016/j.bpj.2018.03.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 02/28/2018] [Accepted: 03/29/2018] [Indexed: 11/16/2022] Open
Abstract
Consensus-designed tetratricopeptide repeat proteins are highly stable, modular proteins that are strikingly amenable to rational engineering. They therefore have tremendous potential as building blocks for biomaterials and biomedicine. Here, we explore the possibility of extending the loops between repeats to enable further diversification, and we investigate how this modification affects stability and folding cooperativity. We find that extending a single loop by up to 25 residues does not disrupt the overall protein structure, but, strikingly, the effect on stability is highly context-dependent: in a two-repeat array, destabilization is relatively small and can be accounted for purely in entropic terms, whereas extending a loop in the middle of a large array is much more costly because of weakening of the interaction between the repeats. Our findings provide important and, to our knowledge, new insights that increase our understanding of the structure, folding, and function of natural repeat proteins and the design of artificial repeat proteins in biotechnology.
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Affiliation(s)
- Albert Perez-Riba
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Alan R Lowe
- London Centre for Nanotechnology, London, United Kingdom; Structural & Molecular Biology, University College London, London, United Kingdom; Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom
| | - Ewan R G Main
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom.
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12
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Wijeratne SS, Nolasco L, Li J, Jiang K, Moake JL, Kiang CH. Correlating Conformational Dynamics with the Von Willebrand Factor Reductase Activity of Factor H Using Single Molecule Force Measurements. J Phys Chem B 2018; 122:10653-10658. [PMID: 30351116 DOI: 10.1021/acs.jpcb.8b06153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Activation of proteins often involves conformational transitions, and these switches are often difficult to characterize in multidomain proteins. Full-length factor H (FH), consisting of 20 small consensus repeat domains (150 kD), is a complement control protein that regulates the activity of the alternative complement pathway. Different preparations of FH can also reduce the disulfide bonds linking large Von Willebrand factor (VWF) multimers into smaller, less adhesive forms. In contrast, commercially available purified FH (pFH) has little or no VWF reductase activity unless the pFH is chemically modified by either ethylenediaminetetraacetic acid (EDTA) or urea. We used atomic force microscopy single molecule force measurements to investigate different forms of FH, including recombinant FH and pFH, in the presence or absence of EDTA and urea, and to correlate the conformational changes to its activities. We found that the FH conformation depends on the method used for sample preparation, which affects the VWF reductase activity of FH.
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13
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Lee M, Choi H, Yoon G, Na S. Loading-device effects on the protein-unfolding mechanisms using molecular-dynamic simulations. J Mol Graph Model 2018; 81:162-167. [PMID: 29554493 DOI: 10.1016/j.jmgm.2018.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/12/2018] [Accepted: 03/10/2018] [Indexed: 10/17/2022]
Abstract
Experimental force spectroscopy has been effectively utilized for measuring structural characterization of biomolecules and mechanical properties of biomaterials. Specifically, atomic force microscopy (AFM) has been widely used to portray biomolecular characterization in single-molecule experiment by observing the unfolding behavior of the proteins. Not only the experimental techniques enable us to characterize globular protein, but computational methods like molecular dynamics (MD) also gives insight into understanding biomolecular structures. To better comprehend the behavior of biomolecules, conditions such as pulling velocities and loading rates are put to the test, yet there are still limitations in understanding the unfolding behavior of biomolecules with the effect of different loading devices. In this study, we performed an all-atom MD and steered molecular dynamics (SMD) simulations considering different loading device effects such as "soft" and "stiff" to characterize the anisotropic unfolding behavior of ubiquitin protein. We found out the anisotropic unfolding pathways of the protein through the broken number of hydrogen bonds and geometric secondary structures of the biomolecule. Our study provides the importance for usage of various loading-devices on biomolecules when analyzing the structural compositions and the characteristics of globular biomolecules.
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Affiliation(s)
- Myeongsang Lee
- Institute of Advanced Machinery Design Technology, Korea University, 02841, Seoul, Republic of Korea
| | - Hyunsung Choi
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea
| | - Gwonchan Yoon
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea; Department of Electrical and Computer Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, 02841, Seoul, Republic of Korea.
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14
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Abstract
Studying protein folding and protein design in globular proteins presents significant challenges because of the two related features, topological complexity and co-operativity. In contrast, tandem-repeat proteins have regular and modular structures composed of linearly arrayed motifs. This means that the biophysics of even giant repeat proteins is highly amenable to dissection and to rational design. Here we discuss what has been learnt about the folding mechanisms of tandem-repeat proteins. The defining features that have emerged are: (i) accessibility of multiple distinct routes between denatured and native states, both at equilibrium and under kinetic conditions; (ii) different routes are favoured for folding compared with unfolding; (iii) unfolding energy barriers are broad, reflecting stepwise unravelling of an array repeat by repeat; (iv) highly co-operative unfolding at equilibrium and the potential for exceptionally high thermodynamic stabilities by introducing consensus residues; (v) under force, helical-repeat structures are very weak with non-co-operative unfolding leading to elasticity and buffering effects. This level of understanding should enable us to create repeat proteins with made-to-measure folding mechanisms, in which one can dial into the sequence the order of repeat folding, number of pathways taken, step size (co-operativity) and fine-structure of the kinetic energy barriers.
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15
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Chen Y, Lee H, Tong H, Schwartz M, Zhu C. Force regulated conformational change of integrin α Vβ 3. Matrix Biol 2016; 60-61:70-85. [PMID: 27423389 DOI: 10.1016/j.matbio.2016.07.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 06/18/2016] [Accepted: 07/08/2016] [Indexed: 11/28/2022]
Abstract
Integrins mediate cell adhesion to extracellular matrix and transduce signals bidirectionally across the membrane. Integrin αVβ3 has been shown to play an essential role in tumor metastasis, angiogenesis, hemostasis and phagocytosis. Integrins can take several conformations, including the bent and extended conformations of the ectodomain, which regulate integrin functions. Using a biomembrane force probe, we characterized the bending and unbending conformational changes of single αVβ3 integrins on living cell surfaces in real-time. We measured the probabilities of conformational changes, rates and speeds of conformational transitions, and the dynamic equilibrium between the two conformations, which were regulated by tensile force, dependent on the ligand, and altered by point mutations. These findings provide insights into how αVβ3 acts as a molecular machine and how its physiological function and molecular structure are coupled at the single-molecule level.
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Affiliation(s)
- Yunfeng Chen
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hyunjung Lee
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Haibin Tong
- Yale Cardiovascular Research Center, Departments of Internal Medicine (Section of Cardiovascular Medicine), Cell Biology and Biomedical Engineering, Yale University, New Haven, CT 06511, USA; Current address: Life Science Research Center, Beihua University, Jilin 132013, China
| | - Martin Schwartz
- Yale Cardiovascular Research Center, Departments of Internal Medicine (Section of Cardiovascular Medicine), Cell Biology and Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Cheng Zhu
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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16
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Cohen SS, Riven I, Cortajarena AL, De Rosa L, D’Andrea LD, Regan L, Haran G. Probing the Molecular Origin of Native-State Flexibility in Repeat Proteins. J Am Chem Soc 2015. [DOI: 10.1021/jacs.5b06160] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sharona S. Cohen
- Chemical
Physics Department, Weizmann institute of Science, Rehovot 76100, Israel
| | - Inbal Riven
- Chemical
Physics Department, Weizmann institute of Science, Rehovot 76100, Israel
| | - Aitziber L. Cortajarena
- IMDEA
Nanociencia, CNB-CSIC-IMDEA Nanociencia Associated Unit “Unidad
de Nanobiotecnología”, Ciudad Universitaria de Cantoblanco, 28049 Madrid, Spain
| | - Lucia De Rosa
- Istituto
di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, via Mezzocannone 16, 80134 Napoli, Italy
| | - Luca D. D’Andrea
- Istituto
di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, via Mezzocannone 16, 80134 Napoli, Italy
| | - Lynne Regan
- Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Gilad Haran
- Chemical
Physics Department, Weizmann institute of Science, Rehovot 76100, Israel
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17
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Li Q, Scholl ZN, Marszalek PE. Capturing the Mechanical Unfolding Pathway of a Large Protein with Coiled-Coil Probes. Angew Chem Int Ed Engl 2014; 53:13429-33. [DOI: 10.1002/anie.201407211] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/10/2014] [Indexed: 11/08/2022]
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18
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Li Q, Scholl ZN, Marszalek PE. Capturing the Mechanical Unfolding Pathway of a Large Protein with Coiled-Coil Probes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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19
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Carballo-Pacheco M, Vancea I, Strodel B. Extension of the FACTS Implicit Solvation Model to Membranes. J Chem Theory Comput 2014; 10:3163-76. [DOI: 10.1021/ct500084y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Martín Carballo-Pacheco
- Forschungszentrum Jülich GmbH, Institute of Complex
Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
| | - Ioan Vancea
- Forschungszentrum Jülich GmbH, Institute of Complex
Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
| | - Birgit Strodel
- Forschungszentrum Jülich GmbH, Institute of Complex
Systems: Structural Biochemistry (ICS-6), 52425 Jülich, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany
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20
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Tamamis P, Terzaki K, Kassinopoulos M, Mastrogiannis L, Mossou E, Forsyth VT, Mitchell EP, Mitraki A, Archontis G. Self-Assembly of an Aspartate-Rich Sequence from the Adenovirus Fiber Shaft: Insights from Molecular Dynamics Simulations and Experiments. J Phys Chem B 2014; 118:1765-74. [DOI: 10.1021/jp409988n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Phanourios Tamamis
- Department
of Physics, University of Cyprus, 75 Kallipoleos Street, CY1678 Nicosia, Cyprus
| | - Konstantina Terzaki
- Department
of Materials Science and Technology, University of Crete, P.O. Box 2208, GR-71003 Heraklion, Crete, Greece
- Institute for Electronic Structure and Laser, FORTH, P.O. Box 1527, GR-71110 Heraklion, Greece
| | - Michalis Kassinopoulos
- Department
of Physics, University of Cyprus, 75 Kallipoleos Street, CY1678 Nicosia, Cyprus
| | - Lefteris Mastrogiannis
- Department
of Materials Science and Technology, University of Crete, P.O. Box 2208, GR-71003 Heraklion, Crete, Greece
- Institute for Electronic Structure and Laser, FORTH, P.O. Box 1527, GR-71110 Heraklion, Greece
| | - Estelle Mossou
- EPSAM/ISTM, Keele University, Keele, Staffordshire ST5
5BG, United Kingdom
- Partnership
for Structural Biology, Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - V. Trevor Forsyth
- EPSAM/ISTM, Keele University, Keele, Staffordshire ST5
5BG, United Kingdom
- Partnership
for Structural Biology, Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
| | - Edward P. Mitchell
- Partnership
for Structural Biology, Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France
- European Synchrotron Radiation Facility, 6 rue Jules Horowitz, 38043 Grenoble Cedex 9, France
| | - Anna Mitraki
- Department
of Materials Science and Technology, University of Crete, P.O. Box 2208, GR-71003 Heraklion, Crete, Greece
- Institute for Electronic Structure and Laser, FORTH, P.O. Box 1527, GR-71110 Heraklion, Greece
| | - Georgios Archontis
- Department
of Physics, University of Cyprus, 75 Kallipoleos Street, CY1678 Nicosia, Cyprus
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21
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Tandem-repeat proteins: regularity plus modularity equals design-ability. Curr Opin Struct Biol 2013; 23:622-31. [PMID: 23831287 DOI: 10.1016/j.sbi.2013.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 12/16/2022]
Abstract
Researchers in the field of rational protein design face a significant challenge, which arises from the two defining and inter-related features of typical globular protein structures, namely topological complexity and cooperativity. In striking contrast to globular proteins, tandem repeat proteins, such as ankyrin, tetratricopeptide and leucine-rich repeats, have regular, modular, linearly arrayed structures which makes it especially straightforward to dissect and redesign their properties. Here we review what we have learnt about the biophysics of natural repeat proteins and recent progress in applying that knowledge to engineer the thermodynamics, folding pathways and molecular recognition properties of tandem repeat proteins, and we discuss the wealth of possibilities presented for the extension of this modular construction process to build new molecules for use in medicine and biotechnology.
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22
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Lehnert BP, Baker AE, Gaudry Q, Chiang AS, Wilson RI. Distinct roles of TRP channels in auditory transduction and amplification in Drosophila. Neuron 2013; 77:115-28. [PMID: 23312520 PMCID: PMC3811118 DOI: 10.1016/j.neuron.2012.11.030] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2012] [Indexed: 11/26/2022]
Abstract
Auditory receptor cells rely on mechanically gated channels to transform sound stimuli into neural activity. Several TRP channels have been implicated in Drosophila auditory transduction, but mechanistic studies have been hampered by the inability to record subthreshold signals from receptor neurons. Here, we develop a non-invasive method for measuring these signals by recording from a central neuron that is electrically coupled to a genetically defined population of auditory receptor cells. We find that the TRPN family member NompC, which is necessary for the active amplification of sound-evoked motion by the auditory organ, is not required for transduction in auditory receptor cells. Instead, NompC sensitizes the transduction complex to movement and precisely regulates the static forces on the complex. In contrast, the TRPV channels Nanchung and Inactive are required for responses to sound, suggesting they are components of the transduction complex. Thus, transduction and active amplification are genetically separable processes in Drosophila hearing.
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Affiliation(s)
- Brendan P Lehnert
- Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA
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23
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The how’s and why’s of protein folding intermediates. Arch Biochem Biophys 2013; 531:14-23. [DOI: 10.1016/j.abb.2012.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/05/2012] [Accepted: 10/11/2012] [Indexed: 12/13/2022]
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24
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25
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Settanni G, Serquera D, Marszalek PE, Paci E, Itzhaki LS. Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin. PLoS Comput Biol 2013; 9:e1002864. [PMID: 23341763 PMCID: PMC3547791 DOI: 10.1371/journal.pcbi.1002864] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 11/11/2012] [Indexed: 11/30/2022] Open
Abstract
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all aspects of the protein's mechanical behavior, including the order of repeat unfolding, the diversity of unfolding pathways accessed, the nature of partially unfolded intermediates, the forces required and the work transferred to the system to unfold the whole protein and its parts. Stepwise unfolding thus provides the means to buffer repeat proteins and their binding partners from mechanical stress in the cell. Our results illustrate how ligand binding can control the mechanical response of proteins. The data also point to a cellular mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress. Here we use molecular dynamics simulation to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with binding partner S6-C. Tandem repeat proteins like Gankyrin comprise tandem arrays of small structural motifs that pack linearly to produce elongated architectures. They are elastic, mechanically weak molecules and they unfold and refold repeat by repeat under force. We show that S6-C binding greatly increases the resistance of Gankyrin to mechanical stress. The enhanced mechanical stability is specific to those ankyrin repeats in contact with S6-C, and the localized nature of the effect results in fundamental changes in the way the protein responds to force. Thus, the forced unfolding of isolated Gankryin involves a diverse set of pathways with a preference for a C- to N-terminus unfolding mechanism whereas this diversity is reduced upon complex formation with the central repeats, which are those most tightly bound to the ligand, tending to unfold last. Our study shows how stepwise unfolding can buffer repeat proteins and their binding partners from mechanical stress in the cell. It also points to a mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.
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Affiliation(s)
- Giovanni Settanni
- Physics Department, Johannes Gutenberg University, Mainz, Germany
- * E-mail: (GS); (EP); (LSI)
| | - David Serquera
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, United States of America
| | - Emanuele Paci
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail: (GS); (EP); (LSI)
| | - Laura S. Itzhaki
- University of Cambridge Department of Chemistry, Cambridge, United Kingdom
- * E-mail: (GS); (EP); (LSI)
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26
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Valbuena A, Vera AM, Oroz J, Menéndez M, Carrión-Vázquez M. Mechanical properties of β-catenin revealed by single-molecule experiments. Biophys J 2012; 103:1744-52. [PMID: 23083718 DOI: 10.1016/j.bpj.2012.07.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 06/20/2012] [Accepted: 07/17/2012] [Indexed: 11/19/2022] Open
Abstract
β-catenin is a central component of the adaptor complex that links cadherins to the actin cytoskeleton in adherens junctions and thus, it is a good candidate to sense and transmit mechanical forces to trigger specific changes inside the cell. To fully understand its molecular physiology, we must first investigate its mechanical role in mechanotransduction within the cadherin system. We have studied the mechanical response of β-catenin to stretching using single-molecule force spectroscopy and molecular dynamics. Unlike most proteins analyzed to date, which have a fixed mechanical unfolding pathway, the β-catenin armadillo repeat region (ARM) displays low mechanostability and multiple alternative unfolding pathways that seem to be modulated by its unstructured termini. These results are supported by steered molecular dynamics simulations, which also predict its mechanical stabilization and unfolding pathway restrictions when the contiguous α-helix of the C-terminal unstructured region is included. Furthermore, simulations of the ARM/E-cadherin cytosolic tail complex emulating the most probable stress geometry occurring in vivo show a mechanical stabilization of the interaction whose magnitude correlates with the length of the stretch of the cadherin cytosolic tail that is in contact with the ARM region.
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Affiliation(s)
- Alejandro Valbuena
- Instituto Cajal/CSIC, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED) and IMDEA Nanociencia, Madrid, Spain
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27
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Heidarsson PO, Valpapuram I, Camilloni C, Imparato A, Tiana G, Poulsen FM, Kragelund BB, Cecconi C. A Highly Compliant Protein Native State with a Spontaneous-like Mechanical Unfolding Pathway. J Am Chem Soc 2012; 134:17068-75. [DOI: 10.1021/ja305862m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pétur O. Heidarsson
- Structural Biology and NMR Laboratory,
Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Immanuel Valpapuram
- Department of Physics, University of Modena and Reggio Emilia, Via Guiseppe
Campi, 41125 Modena, Italy
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge
CB2 1EW, United Kingdom
| | - Alberto Imparato
- Department of Physics and Astronomy, University of Aarhus, Ny Munkegade, Building 1520,
8000 Aarhus C, Denmark
| | - Guido Tiana
- Department
of Physics, University of Milano and INFN, Via Celoria 13, 20133
Milano, Italy
| | - Flemming M. Poulsen
- Structural Biology and NMR Laboratory,
Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory,
Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Ciro Cecconi
- CNR-Nano,
Department of Physics, University of Modena and Reggio Emilia, Via Guiseppe
Campi, 41125 Modena, Italy
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28
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Regulation of the transient receptor potential channel TRPA1 by its N-terminal ankyrin repeat domain. J Mol Model 2012; 19:4689-700. [PMID: 22752543 DOI: 10.1007/s00894-012-1505-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 06/13/2012] [Indexed: 12/31/2022]
Abstract
The transient receptor potential channel A1 (TRPA1) is unique among ion channels of higher vertebrates in that it harbors a large ankyrin repeat domain. The TRPA1 channel is expressed in the inner ear and in nociceptive neurons. It is involved in hearing as well as in the perception of pungent and irritant chemicals. The ankyrin repeat domain has special mechanical properties, which allows it to function as a soft spring that can be extended over a large range while maintaining structural integrity. A calcium-binding site has been experimentally identified within the ankyrin repeats. We built a model of the N-terminal 17 ankyrin repeat structure, including the calcium-binding EF-hand. In our simulations we find the calcium-bound state to be rigid as compared to the calcium-free state. While the end-to-end distance can change by almost 50% in the apo form, these fluctuations are strongly reduced by calcium binding. This increase in stiffness that constraints the end-to-end distance in the holo form is predicted to affect the force acting on the gate of the TRPA1 channel, thereby changing its open probability. Simulations of the transmembrane domain of TRPA1 show that residue N855, which has been associated with familial episodic pain syndrome, forms a strong link between the S4-S5 connecting helix and S1, thereby creating a direct force link between the N-terminus and the gate. The N855S mutation weakens this interaction, thereby reducing the communication between the N-terminus and the transmembrane part of TRPA1.
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29
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Ikeda-Kobayashi A, Taniguchi Y, Brockwell DJ, Paci E, Kawakami M. Prying open single GroES ring complexes by force reveals cooperativity across domains. Biophys J 2012; 102:1961-8. [PMID: 22768953 DOI: 10.1016/j.bpj.2012.03.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/29/2012] [Accepted: 03/14/2012] [Indexed: 11/16/2022] Open
Abstract
Understanding how the mechanical properties of a protein complex emerge from the interplay of intra- and interchain interactions is vital at both fundamental and applied levels. To investigate whether interdomain cooperativity affects protein mechanical strength, we employed single-molecule force spectroscopy to probe the mechanical stability of GroES, a homoheptamer with a domelike quaternary stucture stabilized by intersubunit interactions between the first and last β-strands of adjacent domains. A GroES variant was constructed in which each subunit of the GroES heptamer is covalently linked to adjacent subunits by tripeptide linkers and folded domains of protein L are introduced to the heptamer's termini as handle molecules. The force-distance profiles for GroES unfolding showed, for the first time that we know of, a mechanical phenotype whereby seven distinct force peaks, with alternating behavior of unfolding force and contour length (ΔL(c)), were observed with increasing unfolding-event number. Unfolding of (GroES)(7) is initiated by breakage of the interface between domains 1 and 7 at low force, which imparts a polarity to (GroES)(7) that results in two distinct mechanical phenotypes of these otherwise identical protein domains. Unfolding then proceeds by peeling domains off the domelike native structure by sequential repetition of the denaturation of mechanically weak (unfoldon 1) and strong (unfoldon 2) units. These results indicate that domain-domain interactions help to determine the overall mechanical strength and unfolding pathway of the oligomeric structure. These data reveal an unexpected richness in the mechanical behavior of this homopolyprotein, yielding a complex with greater mechanical strength and properties distinct from those that would be apparent for GroES domains in isolation.
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Affiliation(s)
- Akiko Ikeda-Kobayashi
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan
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30
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Lee W, Strümpfer J, Bennett V, Schulten K, Marszalek PE. Mutation of conserved histidines alters tertiary structure and nanomechanics of consensus ankyrin repeats. J Biol Chem 2012; 287:19115-21. [PMID: 22514283 PMCID: PMC3365944 DOI: 10.1074/jbc.m112.365569] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The conserved TPLH tetrapeptide motif of ankyrin repeats (ARs) plays an important role in stabilizing AR proteins, and histidine (TPLH)-to-arginine (TPLR) mutations in this motif have been associated with a hereditary human anemia, spherocytosis. Here, we used a combination of atomic force microscopy-based single-molecule force spectroscopy and molecular dynamics simulations to examine the mechanical effects of His → Arg substitutions in TPLH motifs in a model AR protein, NI6C. Our molecular dynamics results show that the mutant protein is less mechanically stable than the WT protein. Our atomic force microscopy results indicate that the mechanical energy input necessary to fully unfold the mutant protein is only half of that necessary to unfold the WT protein (53 versus 106 kcal/mol). In addition, the ability of the mutant to generate refolding forces is also reduced. Moreover, the mutant protein subjected to cyclic stretch-relax measurements displays mechanical fatigue, which is absent in the WT protein. Taken together, these results indicate that the His → Arg substitutions in TPLH motifs compromise mechanical properties of ARs and suggest that the origin of hereditary spherocytosis may be related to mechanical failure of ARs.
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Affiliation(s)
- Whasil Lee
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
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31
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Lee W, Zeng X, Rotolo K, Yang M, Schofield CJ, Bennett V, Yang W, Marszalek PE. Mechanical anisotropy of ankyrin repeats. Biophys J 2012; 102:1118-26. [PMID: 22404934 DOI: 10.1016/j.bpj.2012.01.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 01/09/2012] [Accepted: 01/20/2012] [Indexed: 12/19/2022] Open
Abstract
Red blood cells are frequently deformed and their cytoskeletal proteins such as spectrin and ankyrin-R are repeatedly subjected to mechanical forces. While the mechanics of spectrin was thoroughly investigated in vitro and in vivo, little is known about the mechanical behavior of ankyrin-R. In this study, we combine coarse-grained steered molecular dynamics simulations and atomic force spectroscopy to examine the mechanical response of ankyrin repeats (ARs) in a model synthetic AR protein NI6C, and in the D34 fragment of native ankyrin-R when these proteins are subjected to various stretching geometry conditions. Our steered molecular dynamics results, supported by AFM measurements, reveal an unusual mechanical anisotropy of ARs: their mechanical stability is greater when their unfolding is forced to propagate from the N-terminus toward the C-terminus (repeats unfold at ~60 pN), as compared to the unfolding in the opposite direction (unfolding force ∼ 30 pN). This anisotropy is also reflected in the complex refolding behavior of ARs. The origin of this unfolding and refolding anisotropy is in the various numbers of native contacts that are broken and formed at the interfaces between neighboring repeats depending on the unfolding/refolding propagation directions. Finally, we discuss how these complex mechanical properties of ARs in D34 may affect its behavior in vivo.
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Affiliation(s)
- Whasil Lee
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, USA
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32
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Dynamics of protein folding and cofactor binding monitored by single-molecule force spectroscopy. Biophys J 2012; 101:2009-17. [PMID: 22004755 DOI: 10.1016/j.bpj.2011.08.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/23/2011] [Accepted: 08/26/2011] [Indexed: 12/24/2022] Open
Abstract
Many proteins in living cells require cofactors to carry out their biological functions. To reach their functional states, these proteins need to fold into their unique three-dimensional structures in the presence of their cofactors. Two processes, folding of the protein and binding of cofactors, intermingle with each other, making the direct elucidation of the folding mechanism of proteins in the presence of cofactors challenging. Here we use single-molecule atomic force microscopy to directly monitor the folding and cofactor binding dynamics of an engineered metal-binding protein G6-53 at the single-molecule level. Using the mechanical stability of different conformers of G6-53 as sensitive probes, we directly identified different G6-53 conformers (unfolded, apo- and Ni(2+)-bound) populated along the folding pathway of G6-53 in the presence of its cofactor Ni(2+). By carrying out single-molecule atomic force microscopy refolding experiments, we monitored kinetic evolution processes of these different conformers. Our results suggested that the majority of G6-53 folds through a binding-after-folding mechanism, whereas a small fraction follows a binding-before-folding pathway. Our study opens an avenue to utilizing force spectroscopy techniques to probe the folding dynamics of proteins in the presence of cofactors at the single-molecule level, and we anticipated that this method can be used to study a wide variety of proteins requiring cofactors for their function.
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33
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Itzhaki LS, Lowe AR. From artificial antibodies to nanosprings: the biophysical properties of repeat proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 747:153-66. [PMID: 22949117 DOI: 10.1007/978-1-4614-3229-6_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this chapter we review recent studies of repeat proteins, a class of proteins consisting of tandem arrays of small structural motifs that stack approximately linearly to produce elongated structures. We discuss the observation that, despite lacking the long-range tertiary interactions that are thought to be the hallmark of globular protein stability, repeat proteins can be as stable and as co-orperatively folded as their globular counterparts. The symmetry inherent in the structures of repeat arrays, however, means there can be many partly folded species (whether it be intermediates or transition states) that have similar stabilities. Consequently they do have distinct folding properties compared with globular proteins and these are manifest in their behaviour both at equilibrium and under kinetic conditions. Thus, when studying repeat proteins one appears to be probing a moving target: a relatively small perturbation, by mutation for example, can result in a shift to a different intermediate or transition state. The growing literature on these proteins illustrates how their modular architecture can be adapted to a remarkable array of biological and physical roles, both in vivo and in vitro. Further, their simple architecture makes them uniquely amenable to redesign-of their stability, folding and function-promising exciting possibilities for future research.
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Affiliation(s)
- Laura S Itzhaki
- Department of Chemistry, University of Cambridge, Cambridge, UK.
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34
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Liu Y, Hsin J, Kim H, Selvin PR, Schulten K. Extension of a three-helix bundle domain of myosin VI and key role of calmodulins. Biophys J 2011; 100:2964-73. [PMID: 21689530 DOI: 10.1016/j.bpj.2011.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/26/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022] Open
Abstract
The molecular motor protein myosin VI moves toward the minus-end of actin filaments with a step size of 30-36 nm. Such large step size either drastically limits the degree of complex formation between dimer subunits to leave enough length for the lever arms, or requires an extension of the lever arms' crystallographically observed structure. Recent experimental work proposed that myosin VI dimerization triggers the unfolding of the protein's proximal tail domain which could drive the needed lever-arm extension. Here, we demonstrate through steered molecular dynamics simulation the feasibility of sufficient extension arising from turning a three-helix bundle into a long α-helix. A key role is played by the known calmodulin binding that facilitates the extension by altering the strain path in myosin VI. Sequence analysis of the proximal tail domain suggests that further calmodulin binding sites open up when the domain's three-helix bundle is unfolded and that subsequent calmodulin binding stabilizes the extended lever arms.
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Affiliation(s)
- Yanxin Liu
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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35
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Wang CC, Tsong TY, Hsu YH, Marszalek PE. Inhibitor binding increases the mechanical stability of staphylococcal nuclease. Biophys J 2011; 100:1094-9. [PMID: 21320455 DOI: 10.1016/j.bpj.2011.01.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/20/2010] [Accepted: 01/03/2011] [Indexed: 12/19/2022] Open
Abstract
Staphylococcal nuclease (SNase) catalyzes the hydrolysis of DNA and RNA in a calcium-dependent fashion. We used AFM-based single-molecule force spectroscopy to investigate the mechanical stability of SNase alone and in its complex with an SNase inhibitor, deoxythymidine 3',5'-bisphosphate. We found that the enzyme unfolds in an all-or-none fashion at ∼26 pN. Upon binding to the inhibitor, the mechanical unfolding forces of the enzyme-inhibitor complex increase to ∼50 pN. This inhibitor-induced increase in the mechanical stability of the enzyme is consistent with the increased thermodynamical stability of the complex over that of SNase. Because of its strong mechanical response to inhibitor binding, SNase, a model protein folding system, offers a unique opportunity for studying the relationship between enzyme mechanics and catalysis.
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Affiliation(s)
- Chien-Chung Wang
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan, Republic of China. [corrected]
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36
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Graham TGW, Best RB. Force-Induced Change in Protein Unfolding Mechanism: Discrete or Continuous Switch? J Phys Chem B 2011; 115:1546-61. [DOI: 10.1021/jp110738m] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Thomas G. W. Graham
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Robert B. Best
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
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37
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Complex unfolding kinetics of single-domain proteins in the presence of force. Biophys J 2010; 99:1620-7. [PMID: 20816075 PMCID: PMC2931718 DOI: 10.1016/j.bpj.2010.06.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 06/11/2010] [Accepted: 06/17/2010] [Indexed: 02/02/2023] Open
Abstract
Single-molecule force spectroscopy is providing unique, and sometimes unexpected, insights into the free-energy landscapes of proteins. Despite the complexity of the free-energy landscapes revealed by mechanical probes, forced unfolding experiments are often analyzed using one-dimensional models that predict a logarithmic dependence of the unfolding force on the pulling velocity. We previously found that the unfolding force of the protein filamin at low pulling speed did not decrease logarithmically with the pulling speed. Here we present results from a large number of unfolding simulations of a coarse-grain model of the protein filamin under a broad range of constant forces. These show that a two-path model is physically plausible and produces a deviation from the behavior predicted by one-dimensional models analogous to that observed experimentally. We also show that the analysis of the distributions of unfolding forces (p[F]) contains crucial and exploitable information, and that a proper description of the unfolding of single-domain proteins needs to account for the intrinsic multidimensionality of the underlying free-energy landscape, especially when the applied perturbation is small.
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38
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Lee W, Zeng X, Zhou HX, Bennett V, Yang W, Marszalek PE. Full reconstruction of a vectorial protein folding pathway by atomic force microscopy and molecular dynamics simulations. J Biol Chem 2010; 285:38167-72. [PMID: 20870713 DOI: 10.1074/jbc.m110.179697] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
During co-translational folding, the nascent polypeptide chain is extruded sequentially from the ribosome exit tunnel and is [corrected] under severe conformational constraints [corrected] dictated by the one-dimensional geometry of the tunnel. [corrected] How do such vectorial constraints impact the folding pathway? Here, we combine single-molecule atomic force spectroscopy and steered molecular dynamics simulations to examine protein folding in the presence of one-dimensional constraints that are similar to those imposed on the nascent polypeptide chain. The simulations exquisitely reproduced the experimental unfolding and refolding force extension relationships and led to the full reconstruction of the vectorial folding pathway of a large polypeptide, the 253-residue consensus ankyrin repeat protein, NI6C. We show that fully stretched and then relaxed NI6C starts folding by the formation of local secondary structures, followed by the nucleation of three N-terminal repeats. This rate-limiting step is then followed by the vectorial and sequential folding of the remaining repeats. However, after partial unfolding, when allowed to refold, the C-terminal repeats successively regain structures without any nucleation step by using the intact N-terminal repeats as a template. These results suggest a pathway for the co-translational folding of repeat proteins and have implications for mechanotransduction.
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Affiliation(s)
- Whasil Lee
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
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39
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Kim M, Abdi K, Lee G, Rabbi M, Lee W, Yang M, Schofield CJ, Bennett V, Marszalek PE. Fast and forceful refolding of stretched alpha-helical solenoid proteins. Biophys J 2010; 98:3086-92. [PMID: 20550922 DOI: 10.1016/j.bpj.2010.02.054] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2009] [Revised: 02/10/2010] [Accepted: 02/26/2010] [Indexed: 01/23/2023] Open
Abstract
Anfinsen's thermodynamic hypothesis implies that proteins can encode for stretching through reversible loss of structure. However, large in vitro extensions of proteins that occur through a progressive unfolding of their domains typically dissipate a significant amount of energy, and therefore are not thermodynamically reversible. Some coiled-coil proteins have been found to stretch nearly reversibly, although their extension is typically limited to 2.5 times their folded length. Here, we report investigations on the mechanical properties of individual molecules of ankyrin-R, beta-catenin, and clathrin, which are representative examples of over 800 predicted human proteins composed of tightly packed alpha-helical repeats (termed ANK, ARM, or HEAT repeats, respectively) that form spiral-shaped protein domains. Using atomic force spectroscopy, we find that these polypeptides possess unprecedented stretch ratios on the order of 10-15, exceeding that of other proteins studied so far, and their extension and relaxation occurs with minimal energy dissipation. Their sequence-encoded elasticity is governed by stepwise unfolding of small repeats, which upon relaxation of the stretching force rapidly and forcefully refold, minimizing the hysteresis between the stretching and relaxing parts of the cycle. Thus, we identify a new class of proteins that behave as highly reversible nanosprings that have the potential to function as mechanosensors in cells and as building blocks in springy nanostructures. Our physical view of the protein component of cells as being comprised of predominantly inextensible structural elements under tension may need revision to incorporate springs.
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Affiliation(s)
- Minkyu Kim
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems, Duke University, Durham, North Carolina, USA
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40
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Kappel C, Zachariae U, Dölker N, Grubmüller H. An unusual hydrophobic core confers extreme flexibility to HEAT repeat proteins. Biophys J 2010; 99:1596-603. [PMID: 20816072 PMCID: PMC2931736 DOI: 10.1016/j.bpj.2010.06.032] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 05/10/2010] [Accepted: 06/07/2010] [Indexed: 01/16/2023] Open
Abstract
Alpha-solenoid proteins are suggested to constitute highly flexible macromolecules, whose structural variability and large surface area is instrumental in many important protein-protein binding processes. By equilibrium and nonequilibrium molecular dynamics simulations, we show that importin-beta, an archetypical alpha-solenoid, displays unprecedentedly large and fully reversible elasticity. Our stretching molecular dynamics simulations reveal full elasticity over up to twofold end-to-end extensions compared to its bound state. Despite the absence of any long-range intramolecular contacts, the protein can return to its equilibrium structure to within 3 A backbone RMSD after the release of mechanical stress. We find that this extreme degree of flexibility is based on an unusually flexible hydrophobic core that differs substantially from that of structurally similar but more rigid globular proteins. In that respect, the core of importin-beta resembles molten globules. The elastic behavior is dominated by nonpolar interactions between HEAT repeats, combined with conformational entropic effects. Our results suggest that alpha-solenoid structures such as importin-beta may bridge the molecular gap between completely structured and intrinsically disordered proteins.
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Affiliation(s)
| | | | | | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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41
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Understanding biology by stretching proteins: recent progress. Curr Opin Struct Biol 2010; 20:63-9. [PMID: 20138503 DOI: 10.1016/j.sbi.2010.01.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 01/29/2023]
Abstract
Single molecule manipulation techniques combined with molecular dynamics simulations and protein engineering have enabled, during the last decade, the mechanical properties of proteins to be studied directly, thereby giving birth to the field of protein nanomechanics. Recent data obtained from such techniques have helped gain insight into the structural bases of protein resistance against forced unfolding, as well as revealing structural motifs involved in mechanical stability. Also, important technical developments have provided new perspectives into protein folding. Eventually, new and exciting data have shown that mechanical properties are key factors in cell signaling and pathologies, and have been used to rationally tune these properties in a variety of proteins.
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