1
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Liu Z, Liu H, Vera AM, Yang B, Tinnefeld P, Nash MA. Engineering an artificial catch bond using mechanical anisotropy. Nat Commun 2024; 15:3019. [PMID: 38589360 PMCID: PMC11001878 DOI: 10.1038/s41467-024-46858-9] [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: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Catch bonds are a rare class of protein-protein interactions where the bond lifetime increases under an external pulling force. Here, we report how modification of anchor geometry generates catch bonding behavior for the mechanostable Dockerin G:Cohesin E (DocG:CohE) adhesion complex found on human gut bacteria. Using AFM single-molecule force spectroscopy in combination with bioorthogonal click chemistry, we mechanically dissociate the complex using five precisely controlled anchor geometries. When tension is applied between residue #13 on CohE and the N-terminus of DocG, the complex behaves as a two-state catch bond, while in all other tested pulling geometries, including the native configuration, it behaves as a slip bond. We use a kinetic Monte Carlo model with experimentally derived parameters to simulate rupture force and lifetime distributions, achieving strong agreement with experiments. Single-molecule FRET measurements further demonstrate that the complex does not exhibit dual binding mode behavior at equilibrium but unbinds along multiple pathways under force. Together, these results show how mechanical anisotropy and anchor point selection can be used to engineer artificial catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Department of Bionanoscience, Delft University of Technology, 2629HZ, Delft, the Netherlands
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Byeongseon Yang
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland.
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
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2
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Dumas L, Marfoglia M, Yang B, Hijazi M, Larabi AN, Lau K, Pojer F, Nash MA, Barth P. Uncovering and engineering the mechanical properties of the adhesion GPCR ADGRG1 GAIN domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535724. [PMID: 37066252 PMCID: PMC10104041 DOI: 10.1101/2023.04.05.535724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Key cellular functions depend on the transduction of extracellular mechanical signals by specialized membrane receptors including adhesion G-protein coupled receptors (aGPCRs). While recently solved structures support aGPCR activation through shedding of the extracellular GAIN domain, the molecular mechanisms underpinning receptor mechanosensing remain poorly understood. When probed using single-molecule atomic force spectroscopy and molecular simulations, ADGRG1 GAIN dissociated from its tethered agonist at forces significantly higher than other reported signaling mechanoreceptors. Strong mechanical resistance was achieved through specific structural deformations and force propagation pathways under mechanical load. ADGRG1 GAIN variants computationally designed to lock the alpha and beta subdomains and rewire mechanically-induced structural deformations were found to modulate the GPS-Stachel rupture forces. Our study provides unprecedented insights into the molecular underpinnings of GAIN mechanical stability and paves the way for engineering mechanosensors, better understanding aGPCR function, and informing drug-discovery efforts targeting this important receptor class.
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3
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Opdensteinen P, Sperl LE, Mohamadi M, Kündgen‐Redding N, Hagn F, Buyel JF. The transient expression of recombinant proteins in plant cell packs facilitates stable isotope labelling for NMR spectroscopy. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1928-1939. [PMID: 35702941 PMCID: PMC9491462 DOI: 10.1111/pbi.13873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/05/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy can be used to determine the structure, dynamics and interactions of proteins. However, protein NMR requires stable isotope labelling for signal detection. The cells used for the production of recombinant proteins must therefore be grown in medium containing isotopically labelled substrates. Stable isotope labelling is well established in Escherichia coli, but bacteria are only suitable for the production of simple proteins without post-translational modifications. More complex proteins require eukaryotic production hosts, but their growth can be impaired by labelled media, thus reducing product yields and increasing costs. To address this limitation, we used media supplemented with isotope-labelled substrates to cultivate the tobacco-derived cell line BY-2, which was then cast into plant cell packs (PCPs) for the transient expression of a labelled version of the model protein GB1. Mass spectrometry confirmed the feasibility of isotope labelling with 15 N and 2 H using this approach. The resulting NMR spectrum featured a signal dispersion comparable to recombinant GB1 produced in E. coli. PCPs therefore offer a rapid and cost-efficient alternative for the production of isotope-labelled proteins for NMR analysis, especially suitable for complex proteins that cannot be produced in microbial systems.
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Affiliation(s)
- Patrick Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Laura E. Sperl
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Mariam Mohamadi
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | | | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Johannes Felix Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
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4
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Ferenczy GG, Kellermayer M. Contribution of Hydrophobic Interactions to Protein Mechanical Stability. Comput Struct Biotechnol J 2022; 20:1946-1956. [PMID: 35521554 PMCID: PMC9062142 DOI: 10.1016/j.csbj.2022.04.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 11/26/2022] Open
Abstract
The role of hydrophobic and polar interactions in providing thermodynamic stability to folded proteins has been intensively studied, but the relative contribution of these interactions to the mechanical stability is less explored. We used steered molecular dynamics simulations with constant-velocity pulling to generate force-extension curves of selected protein domains and monitor hydrophobic surface unravelling upon extension. Hydrophobic contribution was found to vary between one fifth and one third of the total force while the rest of the contribution is attributed primarily to hydrogen bonds. Moreover, hydrophobic force peaks were shifted towards larger protein extensions with respect to the force peaks attributed to hydrogen bonds. The higher importance of hydrogen bonds compared to hydrophobic interactions in providing mechanical resistance is in contrast with the relative importance of the hydrophobic interactions in providing thermodynamic stability of proteins. The different contributions of these interactions to the mechanical stability are explained by the steeper free energy dependence of hydrogen bonds compared to hydrophobic interactions on the relative positions of interacting atoms. Comparative analyses for several protein domains revealed that the variation of hydrophobic forces is modest, while the contribution of hydrogen bonds to the force peaks becomes increasingly important for mechanically resistant protein domains.
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5
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Mukherjee S, Mondal S, Acharya S, Bagchi B. Tug-of-War between Internal and External Frictions and Viscosity Dependence of Rate in Biological Reactions. PHYSICAL REVIEW LETTERS 2022; 128:108101. [PMID: 35333093 DOI: 10.1103/physrevlett.128.108101] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/13/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The role of water in biological processes is studied in three reactions, namely, the Fe-CO bond rupture in myoglobin, GB1 unfolding, and insulin dimer dissociation. We compute both internal and external components of friction on relevant reaction coordinates. In all of the three cases, the cross-correlation between forces from protein and water is found to be large and negative that serves to reduce the total friction significantly, increase the calculated reaction rate, and weaken solvent viscosity dependence. The computed force spectrum reveals bimodal 1/f noise, suggesting the use of a non-Markovian rate theory.
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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6
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Liu Z, Moreira RA, Dujmović A, Liu H, Yang B, Poma AB, Nash MA. Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex. NANO LETTERS 2022; 22:179-187. [PMID: 34918516 PMCID: PMC8759085 DOI: 10.1021/acs.nanolett.1c03584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/03/2021] [Indexed: 05/27/2023]
Abstract
We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from its target (CTLA-4), by pulling from eight different anchor residues. We found that pulling on the anticalin from residue 60 or 87 resulted in significantly higher rupture forces and a decrease in koff by 2-3 orders of magnitude over a force range of 50-200 pN. Five of the six internal anchor points gave rise to complexes significantly more stable than N- or C-terminal anchor points, rupturing at up to 250 pN at loading rates of 0.1-10 nN s-1. Anisotropic network modeling and molecular dynamics simulations helped to explain the geometric dependency of mechanostability. These results demonstrate that optimization of attachment residue position on therapeutic binding scaffolds can provide large improvements in binding strength, allowing for mechanical affinity maturation under shear stress without mutation of binding interface residues.
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Affiliation(s)
- Zhaowei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Rodrigo A. Moreira
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - Ana Dujmović
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Byeongseon Yang
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Adolfo B. Poma
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
- International
Center for Research on Innovative Biobased Materials (ICRI-BioM)—International
Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Michael A. Nash
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
- National
Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058 Basel, Switzerland
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7
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Arora N, Hazra JP, Rakshit S. Anisotropy in mechanical unfolding of protein upon partner-assisted pulling and handle-assisted pulling. Commun Biol 2021; 4:925. [PMID: 34326473 PMCID: PMC8322310 DOI: 10.1038/s42003-021-02445-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
Proteins as force-sensors respond to mechanical cues and regulate signaling in physiology. Proteins commonly connect the source and response points of mechanical cues in two conformations, independent proteins in end-to-end geometry and protein complexes in handshake geometry. The force-responsive property of independent proteins in end-to-end geometry is studied extensively using single-molecule force spectroscopy (SMFS). The physiological significance of the complex conformations in force-sensing is often disregarded as mere surge protectors. However, with the potential of force-steering, protein complexes possess a distinct mechano-responsive property over individual force-sensors. To decipher, we choose a force-sensing protein, cadherin-23, from tip-link complex and perform SMFS using end-to-end geometry and handshake complex geometry. We measure higher force-resilience of cadherin-23 with preferential shorter extensions in handshake mode of pulling over the direct mode. The handshake geometry drives the force-response of cadherin-23 through different potential-energy landscapes than direct pulling. Analysis of the dynamic network structure of cadherin-23 under tension indicates narrow force-distributions among residues in cadherin-23 in direct pulling, resulting in low force-dissipation paths and low resilience to force. Overall, the distinct and superior mechanical responses of cadherin-23 in handshake geometry than single protein geometry highlight a probable evolutionary drive of protein-protein complexes as force-conveyors over independent ones.
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Affiliation(s)
- Nisha Arora
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
- Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
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8
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Paul S, Venkatramani R. Estimating the Directional Flexibility of Proteins from Equilibrium Thermal Fluctuations. J Chem Theory Comput 2021; 17:3103-3118. [PMID: 33818072 DOI: 10.1021/acs.jctc.0c01070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The directional flexibility of proteins is an equilibrium molecular property which is accessible to both experiment and computation. Single molecule force spectroscopy (SMFS) experiments report effective directional spring constants to describe the collective anisotropic response of a protein structure to mechanical pulling forces applied along selected axes. On the other hand, computational methods have thus far employed either indirect force based nonequilibrium simulations or coarse-grained elastic network models (ENM) to predict protein directional spring constants. Here, we examine the ability of equilibrium atomistic Molecular Dynamics (MD) simulations to estimate the directional flexibility and mechanical anisotropy of proteins. MD-derived effective directional spring constants are found to correlate well with SMFS spring constants (ρ2 = 0.97-0.99; Adj R2 = 0.92-0.99) and unfolding forces (ρ2 = 0.85-0.97; Adj R2 = 0.63-0.91) for five different globular proteins. Specifically, the computed spring constants reproduce the mechanical anisotropy reported by SMFS along five different directions of green fluorescence protein (GFP) and six directions of the immunoglobulin-binding B1 domain of streptococcal protein G (GB1). Further, protein dynamics as captured in MD can be translated into spring constants which can distinguish the N-C directional flexibility of ubiquitin (Ub) from two structurally homologous small ubiquitin-like modifier (SUMO1 and SUMO2) isoforms. We apply our computational framework to study the mechanical anisotropy of Ub along the seven lysine-C-term directions which are functionally relevant. We show that Ub possesses two distinct flexibility scales along these directions which roughly differ by an order of magnitude. Further, our studies reveal that the mechanical anisotropy of Ub is modified in contrasting ways by the binding of two partner proteins (UBCH5A and UEV) which attach and recognize these biomolecular tag proteins. On the basis of equilibrium MD benchmarks for flexibility along 2485 bond vectors in Ub, we propose and validate a new covariance-propagation scheme to extract spring constants from ENM normal modes. We also critically examine the ability of ENM to predict directional flexibility of proteins and suggest modifications to improve these intuitive and scalable descriptions.
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Affiliation(s)
- Sanjoy Paul
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
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9
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Guo Z, Hong H, Yuan G, Qian H, Li B, Cao Y, Wang W, Wu CX, Chen H. Hidden Intermediate State and Second Pathway Determining Folding and Unfolding Dynamics of GB1 Protein at Low Forces. PHYSICAL REVIEW LETTERS 2020; 125:198101. [PMID: 33216575 DOI: 10.1103/physrevlett.125.198101] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Atomic force microscopy experiments found that GB1, a typical two-state model protein used for study of folding and unfolding dynamics, can sustain forces of more than 100 pN, but its response to low forces still remains unclear. Using ultrastable magnetic tweezers, we discovered that GB1 has an unexpected nonmonotonic force-dependent unfolding rate at 5-160 pN, from which a free energy landscape with two main barriers and a hidden intermediate state was constructed. A model combining two separate models by Dudko et al. with two pathways between the native state and this intermediate state is proposed to rebuild the unfolding dynamics over the full experimental force range. One candidate of this transient intermediate state is the theoretically proposed molten globule state with a loosely collapsed conformation, which might exist universally in the folding and unfolding processes of two-state proteins.
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Affiliation(s)
- Zilong Guo
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Haiyan Hong
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Guohua Yuan
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Hui Qian
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Bing Li
- National Laboratory of Solid State Microstructure, Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- National Laboratory of Solid State Microstructure, Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Chen-Xu Wu
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
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10
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Jonchhe S, Ghimire C, Cui Y, Sasaki S, McCool M, Park S, Iida K, Nagasawa K, Sugiyama H, Mao H. Binding of a Telomestatin Derivative Changes the Mechanical Anisotropy of a Human Telomeric G‐Quadruplex. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry and School of Biomedical Sciences Kent State University Kent OH 44240 USA
| | - Chiran Ghimire
- Department of Chemistry & Biochemistry and School of Biomedical Sciences Kent State University Kent OH 44240 USA
| | - Yunxi Cui
- State Key Laboratory of Medicinal Chemical Biology Nankai University Tianjin 300071 China
| | - Shogo Sasaki
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology (TUAT) Koganei Tokyo 184-8588 Japan
| | - Mason McCool
- Department of Chemistry & Biochemistry and School of Biomedical Sciences Kent State University Kent OH 44240 USA
| | - Soyoung Park
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell Material Sciences (iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Keisuke Iida
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology (TUAT) Koganei Tokyo 184-8588 Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science Faculty of Technology Tokyo University of Agriculture and Technology (TUAT) Koganei Tokyo 184-8588 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell Material Sciences (iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Hanbin Mao
- Department of Chemistry & Biochemistry and School of Biomedical Sciences Kent State University Kent OH 44240 USA
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11
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Jonchhe S, Ghimire C, Cui Y, Sasaki S, McCool M, Park S, Iida K, Nagasawa K, Sugiyama H, Mao H. Binding of a Telomestatin Derivative Changes the Mechanical Anisotropy of a Human Telomeric G-Quadruplex. Angew Chem Int Ed Engl 2018; 58:877-881. [PMID: 30476359 DOI: 10.1002/anie.201811046] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Indexed: 01/31/2023]
Abstract
Mechanical anisotropy is an essential property for biomolecules to assume structural and functional roles in mechanobiology. However, there is insufficient information on the mechanical anisotropy of ligand-biomolecule complexes. Herein, we investigated the mechanical property of individual human telomeric G-quadruplexes bound to telomestatin, using optical tweezers. Stacking of the ligand to the G-tetrad planes changes the conformation of the G-quadruplex, which resembles a balloon squeezed in certain directions. Such a squeezed balloon effect strengthens the G-tetrad planes, but dislocates and weakens the loops in the G-quadruplex upon ligand binding. These dynamic interactions indicate that the binding between the ligand and G-quadruplex follows the induced-fit model. We anticipate that the altered mechanical anisotropy of the ligand-G-quadruplex complex can add additional level of regulations on the motor enzymes that process DNA or RNA molecules.
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Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44240, USA
| | - Chiran Ghimire
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44240, USA
| | - Yunxi Cui
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Shogo Sasaki
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo, 184-8588, Japan
| | - Mason McCool
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44240, USA
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Keisuke Iida
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo, 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), Koganei, Tokyo, 184-8588, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hanbin Mao
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, OH, 44240, USA
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12
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Izadi D, Chen Y, Whitmore ML, Slivka JD, Ching K, Lapidus LJ, Comstock MJ. Combined Force Ramp and Equilibrium High-Resolution Investigations Reveal Multipath Heterogeneous Unfolding of Protein G. J Phys Chem B 2018; 122:11155-11165. [DOI: 10.1021/acs.jpcb.8b06199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Dena Izadi
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yujie Chen
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Miles L. Whitmore
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Joseph D. Slivka
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin Ching
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lisa J. Lapidus
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
| | - Matthew J. Comstock
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United States
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13
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Nassar R, Wong E, Bui JM, Yip CK, Li H, Gsponer J, Lamour G. Mechanical Anisotropy in GNNQQNY Amyloid Crystals. J Phys Chem Lett 2018; 9:4901-4909. [PMID: 30102541 DOI: 10.1021/acs.jpclett.8b02027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mapping the nanomechanical properties of amyloids can provide valuable insights into structure and assembly mechanisms of protein aggregates that underlie the development of various human diseases. Although it is well-known that amyloids exhibit an intrinsic stiffness comparable to that of silk (1-10 GPa), a detailed understanding of the directional dependence (anisotropy) of the stiffness of amyloids and how it relates to structural features in these protein aggregates is missing. Here we used steered molecular dynamics (SMD) simulations and amplitude modulation-frequency modulation (AM-FM) atomic force microscopy to measure the directional variation in stiffness of GNNQQNY amyloid crystals. We reveal that individual crystals display significant mechanical anisotropy and relate this anisotropy to subtle but mechanically important differences in interactions between interfaces that define the crystal architecture. Our results provide detailed insights into the structure-mechanics relationship of amyloid that may help in designing amyloid-based nanomaterials with tailored mechanical properties.
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Affiliation(s)
- Roy Nassar
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Eric Wong
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Jennifer M Bui
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Calvin K Yip
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Hongbin Li
- Department of Chemistry , The University of British Columbia , Vancouver , BC Canada V6T 1Z1
| | - Jörg Gsponer
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Guillaume Lamour
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
- Department of Chemistry , The University of British Columbia , Vancouver , BC Canada V6T 1Z1
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14
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Nunes-Alves A, Arantes GM. Mechanical Unfolding of Macromolecules Coupled to Bond Dissociation. J Chem Theory Comput 2017; 14:282-290. [DOI: 10.1021/acs.jctc.7b00805] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ariane Nunes-Alves
- Department of Biochemistry,
Instituto de Quı́mica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Guilherme Menegon Arantes
- Department of Biochemistry,
Instituto de Quı́mica, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
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15
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Sun Y, Di W, Li Y, Huang W, Wang X, Qin M, Wang W, Cao Y. Mg2+-Dependent High Mechanical Anisotropy of Three-Way-Junction pRNA as Revealed by Single-Molecule Force Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yang Sun
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Weishuai Di
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Yiran Li
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Xin Wang
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures; National Laboratory of Solid State Microstructure; Department of Physics; Nanjing University; 22 Hankou Road Nanjing Jiang Su 210093 P.R. China
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16
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Sun Y, Di W, Li Y, Huang W, Wang X, Qin M, Wang W, Cao Y. Mg 2+ -Dependent High Mechanical Anisotropy of Three-Way-Junction pRNA as Revealed by Single-Molecule Force Spectroscopy. Angew Chem Int Ed Engl 2017. [PMID: 28631866 DOI: 10.1002/anie.201704113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mechanical anisotropy is ubiquitous in biological tissues but is hard to reproduce in synthetic biomaterials. Developing molecular building blocks with anisotropic mechanical response is the key towards engineering anisotropic biomaterials. The three-way-junction (3WJ) pRNA, derived from ϕ29 DNA packaging motor, shows strong mechanical anisotropy upon Mg2+ binding. In the absence of Mg2+ , 3WJ-pRNA is mechanically weak without noticeable mechanical anisotropy. In the presence of Mg2+ , the unfolding forces can differ by more than 4-fold along different pulling directions, ranging from about 47 pN to about 219 pN. Mechanical anisotropy of 3WJ-pRNA stems from pulling direction dependent cooperativity for the rupture of two Mg2+ binding sites, which is a novel mechanism for the mechanical anisotropy of biomacromolecules. It is anticipated that 3WJ-pRNA can be used as a key element for the construction of biomaterials with controllable mechanical anisotropy.
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Affiliation(s)
- Yang Sun
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Weishuai Di
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Yiran Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Wenmao Huang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Xin Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, 22 Hankou Road, Nanjing, Jiang Su, 210093, P.R. China
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17
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Berkovich R, Mondal J, Paster I, Berne BJ. Simulated Force Quench Dynamics Shows GB1 Protein Is Not a Two State Folder. J Phys Chem B 2017; 121:5162-5173. [PMID: 28453938 DOI: 10.1021/acs.jpcb.7b00610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single molecule force spectroscopy is a useful technique for investigating mechanically induced protein unfolding and refolding under reduced forces by monitoring the end-to-end distance of the protein. The data is often interpreted via a "two-state" model based on the assumption that the end-to-end distance alone is a good reaction coordinate and the thermodynamic behavior is then ascribed to the free energy as a function of this one reaction coordinate. In this paper, we determined the free energy surface (PMF) of GB1 protein from atomistic simulations in explicit solvent under different applied forces as a function of two collective variables (the end-to-end-distance, and the fraction of native contacts ρ). The calculated 2-d free energy surfaces exhibited several distinct states, or basins, mostly visible along the ρ coordinate. Brownian dynamics (BD) simulations on the smoothed free energy surface show that the protein visits a metastable molten globule state and is thus a three state folder, not the two state folder inferred using the end-to-end distance as the sole reaction coordinate. This study lends support to recent experiments that suggest that GB1 is not a two-state folder.
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Affiliation(s)
- Ronen Berkovich
- Department of Chemical Engineering, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences , Hyderabad, India
| | - Inga Paster
- Department of Chemical Engineering, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - B J Berne
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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18
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Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation. J Mol Model 2016; 22:188. [DOI: 10.1007/s00894-016-3052-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
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19
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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20
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Kravats AN, Tonddast-Navaei S, Stan G. Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines. PLoS Comput Biol 2016; 12:e1004675. [PMID: 26734937 PMCID: PMC4703411 DOI: 10.1371/journal.pcbi.1004675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/25/2015] [Indexed: 01/30/2023] Open
Abstract
Clp ATPases are powerful ring shaped nanomachines which participate in the degradation pathway of the protein quality control system, coupling the energy from ATP hydrolysis to threading substrate proteins (SP) through their narrow central pore. Repetitive cycles of sequential intra-ring ATP hydrolysis events induce axial excursions of diaphragm-forming central pore loops that effect the application of mechanical forces onto SPs to promote unfolding and translocation. We perform Langevin dynamics simulations of a coarse-grained model of the ClpY ATPase-SP system to elucidate the molecular details of unfolding and translocation of an α/β model protein. We contrast this mechanism with our previous studies which used an all-α SP. We find conserved aspects of unfolding and translocation mechanisms by allosteric ClpY, including unfolding initiated at the tagged C-terminus and translocation via a power stroke mechanism. Topology-specific aspects include the time scales, the rate limiting steps in the degradation pathway, the effect of force directionality, and the translocase efficacy. Mechanisms of ClpY-assisted unfolding and translocation are distinct from those resulting from non-allosteric mechanical pulling. Bulk unfolding simulations, which mimic Atomic Force Microscopy-type pulling, reveal multiple unfolding pathways initiated at the C-terminus, N-terminus, or simultaneously from both termini. In a non-allosteric ClpY ATPase pore, mechanical pulling with constant velocity yields larger effective forces for SP unfolding, while pulling with constant force results in simultaneous unfolding and translocation. Cell survival is critically dependent on tightly regulated protein quality control, which includes chaperone-mediated folding and degradation. In the degradation pathway, AAA+ nanomachines, such as bacterial Clp proteases, use ATP-driven mechanisms to mechanically unfold, translocate, and destroy excess or defective proteins. Understanding these remodeling mechanisms is of central importance for deciphering the details of essential cellular processes. We perform coarse-grained computer simulations to extensively probe the effect of substrate protein topology on unfolding and translocation actions of the ClpY ATPase nanomachine. We find that, independent of SP topology, unfolding proceeds from the tagged C-terminus, which is engaged by the ATPase, and translocation involves coordinated steps. Topology-specific aspects include more complex unfolding and translocation pathways of the α/β SP compared with the all-α SP due to high stability of β-hairpins and interplay of tertiary contacts. In addition, directionality of the mechanical force applied by the Clp ATPase gives rise to distinct unfolding pathways.
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Affiliation(s)
- Andrea N. Kravats
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Sam Tonddast-Navaei
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
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21
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Baumann F, Bauer MS, Milles LF, Alexandrovich A, Gaub HE, Pippig DA. Monovalent Strep-Tactin for strong and site-specific tethering in nanospectroscopy. NATURE NANOTECHNOLOGY 2016; 11:89-94. [PMID: 26457965 DOI: 10.1038/nnano.2015.231] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 09/03/2015] [Indexed: 06/05/2023]
Abstract
Strep-Tactin, an engineered form of streptavidin, binds avidly to the genetically encoded peptide Strep-tag II in a manner comparable to streptavidin binding to biotin. These interactions have been used in protein purification and detection applications. However, in single-molecule studies, for example using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), the tetravalency of these systems impedes the measurement of monodispersed data. Here, we introduce a monovalent form of Strep-Tactin that harbours a unique binding site for Strep-tag II and a single cysteine that allows Strep-Tactin to specifically attach to the atomic force microscope cantilever and form a consistent pulling geometry to obtain homogeneous rupture data. Using AFM-SMFS, the mechanical properties of the interaction between Strep-tag II and monovalent Strep-Tactin were characterized. Rupture forces comparable to biotin:streptavidin unbinding were observed. Using titin kinase and green fluorescent protein, we show that monovalent Strep-Tactin is generally applicable to protein unfolding experiments. We expect monovalent Strep-Tactin to be a reliable anchoring tool for a range of single-molecule studies.
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Affiliation(s)
- Fabian Baumann
- Center for Nanoscience and Department of Physics, Ludwig Maximilians University of Munich, Amalienstraße 54, Munich 80799, Germany
| | - Magnus S Bauer
- Center for Nanoscience and Department of Physics, Ludwig Maximilians University of Munich, Amalienstraße 54, Munich 80799, Germany
| | - Lukas F Milles
- Center for Nanoscience and Department of Physics, Ludwig Maximilians University of Munich, Amalienstraße 54, Munich 80799, Germany
| | - Alexander Alexandrovich
- Randall Division of Cell and Molecular Biophysics and Cardiovascular Division, New Hunt's House, King's College London, London SE1 1UL, UK
| | - Hermann E Gaub
- Center for Nanoscience and Department of Physics, Ludwig Maximilians University of Munich, Amalienstraße 54, Munich 80799, Germany
| | - Diana A Pippig
- Center for Nanoscience and Department of Physics, Ludwig Maximilians University of Munich, Amalienstraße 54, Munich 80799, Germany
- Center for Integrated Protein Science Munich, Ludwig Maximilians University of Munich, Butenandtstraße 5-13, Munich 81377, Germany
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22
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Schoeler C, Bernardi RC, Malinowska KH, Durner E, Ott W, Bayer EA, Schulten K, Nash MA, Gaub HE. Mapping Mechanical Force Propagation through Biomolecular Complexes. NANO LETTERS 2015; 15:7370-6. [PMID: 26259544 PMCID: PMC4721519 DOI: 10.1021/acs.nanolett.5b02727] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Here we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. The results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.
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23
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Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK. Proc Natl Acad Sci U S A 2015; 112:10389-94. [PMID: 26240360 DOI: 10.1073/pnas.1504625112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The regulation of protein function through ligand-induced conformational changes is crucial for many signal transduction processes. The binding of a ligand alters the delicate energy balance within the protein structure, eventually leading to such conformational changes. In this study, we elucidate the energetic and mechanical changes within the subdomains of the nucleotide binding domain (NBD) of the heat shock protein of 70 kDa (Hsp70) chaperone DnaK upon nucleotide binding. In an integrated approach using single molecule optical tweezer experiments, loop insertions, and steered coarse-grained molecular simulations, we find that the C-terminal helix of the NBD is the major determinant of mechanical stability, acting as a glue between the two lobes. After helix unraveling, the relative stability of the two separated lobes is regulated by ATP/ADP binding. We find that the nucleotide stays strongly bound to lobe II, thus reversing the mechanical hierarchy between the two lobes. Our results offer general insights into the nucleotide-induced signal transduction within members of the actin/sugar kinase superfamily.
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24
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Caldwell TA, Sumner I, Wright NT. Mechanical dissociation of the M-band titin/obscurin complex is directionally dependent. FEBS Lett 2015; 589:1735-9. [PMID: 26001486 DOI: 10.1016/j.febslet.2015.05.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 11/29/2022]
Abstract
Titin and obscurin, two giant muscle proteins, bind to each other in an antiparallel Ig-Ig fashion at the M-band. This interaction must be able to withstand the mechanical strain that the M-band typically experiences and remain intact. The mechanical force on these domains is likely exerted along one of two axes: a longitudinal axis, resulting in a 'shearing' force, or a lateral axis, resulting in a 'peeling' force. Here we present molecular dynamics data suggesting that these forces result in distinct unraveling pathways of the titin/obscurin complex and that peeling the domains apart requires less work and force.
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Affiliation(s)
- Tracy A Caldwell
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr., Harrisonburg, VA 22807, United States
| | - Isaiah Sumner
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr., Harrisonburg, VA 22807, United States
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Dr., Harrisonburg, VA 22807, United States.
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25
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Crépin T, Swale C, Monod A, Garzoni F, Chaillet M, Berger I. Polyproteins in structural biology. Curr Opin Struct Biol 2015; 32:139-46. [PMID: 25996897 PMCID: PMC7125721 DOI: 10.1016/j.sbi.2015.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 04/23/2015] [Accepted: 04/27/2015] [Indexed: 12/21/2022]
Abstract
Structures have been determined for natural and recombinant polyproteins. Native HIV Gag polyprotein architecture was revealed by cryo-EM of immature capsids. Recombinant polyprotein technology has resolved sample preparation bottlenecks. The high-resolution structure of influenza polymerase has been solved. Single-molecule analysis of polyproteins revealed their folding characteristics.
Polyproteins are chains of covalently conjoined smaller proteins that occur in nature as versatile means to organize the proteome of viruses including HIV. During maturation, viral polyproteins are typically cleaved into the constituent proteins with different biological functions by highly specific proteases, and structural analyses at defined stages of this maturation process can provide clues for antiviral intervention strategies. Recombinant polyproteins that use similar mechanisms are emerging as powerful tools for producing hitherto inaccessible protein targets such as the influenza polymerase, for high-resolution structure determination by X-ray crystallography. Conversely, covalent linking of individual protein subunits into single polypeptide chains are exploited to overcome sample preparation bottlenecks. Moreover, synthetic polyproteins provide a promising tool to dissect dynamic folding of polypeptide chains into three-dimensional architectures in single-molecule structure analysis by atomic force microscopy (AFM). The recent use of natural and synthetic polyproteins in structural biology and major achievements are highlighted in this contribution.
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Affiliation(s)
- Thibaut Crépin
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France.
| | - Christopher Swale
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Alexandre Monod
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Frederic Garzoni
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; The European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France
| | - Maxime Chaillet
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; The European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France
| | - Imre Berger
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; The European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France; The School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom.
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26
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Farrance OE, Paci E, Radford SE, Brockwell DJ. Extraction of accurate biomolecular parameters from single-molecule force spectroscopy experiments. ACS NANO 2015; 9:1315-1324. [PMID: 25646767 DOI: 10.1021/nn505135d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The atomic force microscope (AFM) is able to manipulate biomolecules and their complexes with exquisite force sensitivity and distance resolution. This capability, complemented by theoretical models, has greatly improved our understanding of the determinants of mechanical strength in proteins and revealed the diverse effects of directional forces on the energy landscape of biomolecules. In unbinding experiments, the interacting partners are usually immobilized on their respective substrates via extensible linkers. These linkers affect both the force and contour length (Lc) of the complex at rupture. Surprisingly, while the former effect is well understood, the latter is largely neglected, leading to incorrect estimations of Lc, a parameter that is often used as evidence for the detection of specific interactions and remodeling events and for the inference of interaction regions. To address this problem, a model that predicts contour length measurements from single-molecule forced-dissociation experiments is presented that considers attachment position on the AFM tip, geometric effects, and polymer dynamics of the linkers. Modeled data are compared with measured contour length distributions from several different experimental systems, revealing that current methods underestimate contour lengths. The model enables nonspecific interactions to be identified unequivocally, allows accurate determination of Lc, and, by comparing experimental and modeled distributions, enables partial unfolding events before rupture to be identified unequivocally.
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Affiliation(s)
- Oliver E Farrance
- Astbury Centre for Structural and Molecular Biology and School of Molecular and Cellular Biology, University of Leeds , Leeds, West Yorkshire, LS2 9JT, U.K
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27
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Chen Y, Radford SE, Brockwell DJ. Force-induced remodelling of proteins and their complexes. Curr Opin Struct Biol 2015; 30:89-99. [PMID: 25710390 PMCID: PMC4499843 DOI: 10.1016/j.sbi.2015.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 11/23/2022]
Abstract
Force can drive conformational changes in proteins, as well as modulate their stability and the affinity of their complexes, allowing a mechanical input to be converted into a biochemical output. These properties have been utilised by nature and force is now recognised to be widely used at the cellular level. The effects of force on the biophysical properties of biological systems can be large and varied. As these effects are only apparent in the presence of force, studies on the same proteins using traditional ensemble biophysical methods can yield apparently conflicting results. Where appropriate, therefore, force measurements should be integrated with other experimental approaches to understand the physiological context of the system under study.
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Affiliation(s)
- Yun Chen
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School 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; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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28
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Zheng P, Chou CC, Guo Y, Wang Y, Li H. Single Molecule Force Spectroscopy Reveals the Molecular Mechanical Anisotropy of the FeS4 Metal Center in Rubredoxin. J Am Chem Soc 2013; 135:17783-92. [DOI: 10.1021/ja406695g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peng Zheng
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Chih-Chung Chou
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Ying Guo
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
| | - Yanyan Wang
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 30072 P. R. China
| | - Hongbin Li
- Department
of Chemistry, University of British Columbia Vancouver, British Columbia V6T 1Z1, Canada
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 30072 P. R. China
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Dehouck Y, Mikhailov AS. Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics. PLoS Comput Biol 2013; 9:e1003209. [PMID: 24009495 PMCID: PMC3757084 DOI: 10.1371/journal.pcbi.1003209] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/19/2013] [Indexed: 11/18/2022] Open
Abstract
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or on their ability to perform wider and sometimes highly elaborated motions. Hence, there is considerable interest in the definition of accurate coarse-grained descriptions of protein dynamics, as an alternative to more computationally expensive approaches. In particular, the elastic network model, in which residue motions are subjected to pairwise harmonic potentials, is known to capture essential aspects of conformational dynamics in proteins, but has so far remained mostly phenomenological, and unable to account for the chemical specificities of amino acids. We propose, for the first time, a method to derive residue- and distance-specific effective harmonic potentials from the statistical analysis of an extensive dataset of NMR conformational ensembles. These potentials constitute dynamical counterparts to the mean-force statistical potentials commonly used for static analyses of protein structures. In the context of the elastic network model, they yield a strongly improved description of the cooperative aspects of residue motions, and give the opportunity to systematically explore the influence of sequence details on protein dynamics.
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Affiliation(s)
- Yves Dehouck
- Department of Physical Chemistry, Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany.
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