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Dong L, Li L, Chen H, Cao Y, Lei H. Mechanochemistry: Fundamental Principles and Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403949. [PMID: 39206931 DOI: 10.1002/advs.202403949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/30/2024] [Indexed: 09/04/2024]
Abstract
Mechanochemistry is an emerging research field at the interface of physics, mechanics, materials science, and chemistry. Complementary to traditional activation methods in chemistry, such as heat, electricity, and light, mechanochemistry focuses on the activation of chemical reactions by directly or indirectly applying mechanical forces. It has evolved as a powerful tool for controlling chemical reactions in solid state systems, sensing and responding to stresses in polymer materials, regulating interfacial adhesions, and stimulating biological processes. By combining theoretical approaches, simulations and experimental techniques, researchers have gained intricate insights into the mechanisms underlying mechanochemistry. In this review, the physical chemistry principles underpinning mechanochemistry are elucidated and a comprehensive overview of recent significant achievements in the discovery of mechanically responsive chemical processes is provided, with a particular emphasis on their applications in materials science. Additionally, The perspectives and insights into potential future directions for this exciting research field are offered.
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Affiliation(s)
- Liang Dong
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu, 210093, P. R. China
| | - Luofei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu, 210093, P. R. China
| | - Huiyan Chen
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu, 210093, P. R. China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu, 210093, P. R. China
| | - Hai Lei
- School of Physics, Zhejiang University, Hangzhou, Zhejiang, 310027, P. R. China
- Institute of Advanced Physics, Zhejiang University, Hangzhou, Zhejiang, 310027, P. R. China
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Zhang Z, Zhao W, Cheng Z, Zhang G, Liu H. Olympic gels formed through catenation of dsDNA rings regulated by topoisomerase II: A coarse-grained model. J Chem Phys 2024; 160:054906. [PMID: 38341711 DOI: 10.1063/5.0190580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024] Open
Abstract
Topological regulation of DNA by topoisomerases in cells is very crucial for life. We propose a coarse-grained model to study the catenation process of double-stranded DNA (dsDNA) rings regulated by topoisomerase II (TOP2) and provide a computational method to characterize the topological structures of the Olympic gels obtained. The function of TOP2 in the catenation of dsDNA rings is implicitly fulfilled by operating the length of a stretchable catch bond in the dsDNA ring. After the catenation reaction of initially noncatenated dsDNA rings in the solution, the Olympic gel is obtained and the interlocked topology of the dsDNA rings can be characterized by a computational method derived from the HOMFLY polynomial, based on which the catenation degree and the complexity of catenation are quantified. Detailed dependence of the catenation degree and the complexity of the catenated topology on key parameters, including the size of the transient broken gap and the duration time of the break on the dsDNA ring during operation by TOP2, the initial molar ratio of TOP2 to the dsDNA rings, and the reaction temperature, has been investigated.
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Affiliation(s)
- Zhongyan Zhang
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
- School of Chemistry, South China Normal University, Guangzhou 510006, China
| | - Wenbo Zhao
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
| | - Zhiyuan Cheng
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
| | - Guojie Zhang
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Hong Liu
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
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3
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Yang X, Zhang D, Liu R, Wang L, Liu JY, Wang Z. Rapid Thalidomide Racemization Is Related to Proton Tunneling Reactions via Water Bridges. J Phys Chem Lett 2023; 14:10592-10598. [PMID: 37976462 DOI: 10.1021/acs.jpclett.3c02757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Quantum mechanical tunneling (QMT) can play an important role in light element-related chemical reactions; however, its influence on racemization is not fully understood. Herein, we demonstrate that the role of QMT is decisive for rapid racemization of the well-known thalidomide molecule in aqueous environments, increasing the reaction rate constants of the most likely racemization pathways by 87-149 times at approximately body temperature and achieving good agreement between theoretical calculations and experimental observations. In addition, the kinetic isotope effect values fit well with those of previous experiments. These results are attributed to enhanced tunneling probability due to the alteration of potential barriers for proton transfer reactions via water bridges. This work highlights the significance of the QMT effect in racemization and its potential impact on drug safety, providing a fundamental perspective for understanding chirality-related issues in biological systems.
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Affiliation(s)
- Xinrui Yang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
| | - Depeng Zhang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Normal School, Shenyang University, Shenyang 110044, China
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education, College of Physics, Jilin University, Changchun 130012, China
| | - Rui Liu
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education, College of Physics, Jilin University, Changchun 130012, China
| | - Lu Wang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
| | - Jing-Yao Liu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
- Key Laboratory of Material Simulation Methods & Software of Ministry of Education, College of Physics, Jilin University, Changchun 130012, China
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Nwoye E, Raghuraman S, Costales M, Batteas J, Felts JR. Mechanistic model for quantifying the effect of impact force on mechanochemical reactivity. Phys Chem Chem Phys 2023; 25:29088-29097. [PMID: 37862006 DOI: 10.1039/d3cp02549g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Conventional mechanochemical synthetic tools, such as ball mills, offer no methodology to quantitatively link macroscale reaction parameters, such as shaking frequency or milling ball radius, to fundamental drivers of reactivity, namely the force vectors applied to the reactive molecules. As a result, although mechanochemistry has proven to be a valuable method to make a wide variety of products, the results are seldom reproduceable between reactors, difficult to rationally optimize, and hard to ascribe to a specific reaction pathway. Here we have developed a controlled force reactor, which is a mechanochemical ball mill reactor with integrated force measurement and control during each impact. We relate two macroscale reactor parameters-impact force and impact time-to thermodynamic and kinetic transition state theories of mechanochemistry utilizing continuum contact mechanics principles. We demonstrate force controlled particle fracture of NaCl to characterize particle size evolution during reactions, and force controlled reaction between anhydrous copper(II) chloride and (1, 10) phenanthroline. During the fracture of NaCl, we monitor the evolution of particle size as a function of impact force and find that particles quickly reach a particle size of ∼100 μm largely independent of impact force, and reach steady state 10-100× faster than reaction kinetics of typical mechanochemical reactions. We monitor the copper(II) chloride reactivity by measuring color change during reaction. Applying our transition state theory developed here to the reaction curves of copper(II) chloride and (1, 10) phenanthroline at multiple impact forces results in an activation energy barrier of 0.61 ± 0.07 eV, distinctly higher than barriers for hydrated metal salts and organic ligands and distinctly lower than the direct cleavage of the CuCl bond, indicating that the reaction may be mediated by the higher affinity of Fe in the stainless steel vessel to Cl. We further show that the results in the controlled force reactor match rudimentary estimations of impact force within a commercial ball mill reactor Retsch MM400. These results demonstrate the ability to quantitatively link macroscale reactor parameters to reaction properties, motivating further work to make mechanochemical synthesis quantitative, predictable, and fundamentally insightful.
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Affiliation(s)
- Emmanuel Nwoye
- Advanced Nanomanufacturing Laboratory, Department of Mechanical Engineering, Texas A&M University, College Station, Texas-77843-3123, USA.
| | | | - Maya Costales
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - James Batteas
- Department of Chemistry, Texas A&M University, College Station, TX 77842, USA
| | - Jonathan R Felts
- Advanced Nanomanufacturing Laboratory, Department of Mechanical Engineering, Texas A&M University, College Station, Texas-77843-3123, USA.
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Lee MH, Tsai HP, Lavy C, Mouthuy PA, Czernuszka J. Time-dependent extracellular matrix alterations of young tendons in response to stress relaxation: a model for the Ponseti method. J R Soc Interface 2023; 20:20220712. [PMID: 37194273 PMCID: PMC10189311 DOI: 10.1098/rsif.2022.0712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/06/2023] [Indexed: 05/18/2023] Open
Abstract
The Ponseti method corrects a clubfoot by manipulation and casting which causes stress relaxation on the tendons. Here, we examined the effect of long-term stress relaxation on tendon extracellular matrix (ECM) by (1) an ex vivo stress relaxation test, (2) an in vitro tenocyte culture with stress relaxation and (3) an in vivo rabbit study. Time-dependent tendon lengthening and ECM alterations including crimp angle reduction and cleaved elastin were observed, which illustrated the mechanism of tissue lengthening behind the treatment-a material-based crimp angle reduction resulted from elastin cleavage. Additionally, in vitro and in vivo results observed restoration of these ECM alterations along with increased elastin level after 7 days of treatment, and the existence of neovascularization and inflammation, indicating the recovery and adaptation from the tendon in reaction to the treatment. Overall, this study provides the scientific background and information that helps explain the Ponseti method.
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Affiliation(s)
- Mu-Huan Lee
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
| | - Hung-Pei Tsai
- Division of Neurosurgery, Department of Surgery, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chris Lavy
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, Botnar Research Centre, University of Oxford, Windmill Road, Oxford OX3 7LD, UK
| | - Pierre-Alexis Mouthuy
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science, Botnar Research Centre, University of Oxford, Windmill Road, Oxford OX3 7LD, UK
| | - Jan Czernuszka
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
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Shah A, Ghalsasi PS, Ghalsasi P. Effect of quasi hydrostatic and non hydrostatic pressure on long S–S bonded sodium dithionite (Na2S2O4): A Raman Spectroscopic study. J SOLID STATE CHEM 2022. [DOI: 10.1016/j.jssc.2022.123315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mulla Y, Avellaneda MJ, Roland A, Baldauf L, Jung W, Kim T, Tans SJ, Koenderink GH. Weak catch bonds make strong networks. NATURE MATERIALS 2022; 21:1019-1023. [PMID: 36008604 PMCID: PMC7613626 DOI: 10.1038/s41563-022-01288-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 05/11/2022] [Indexed: 05/12/2023]
Abstract
Molecular catch bonds are ubiquitous in biology and essential for processes like leucocyte extravasion1 and cellular mechanosensing2. Unlike normal (slip) bonds, catch bonds strengthen under tension. The current paradigm is that this feature provides 'strength on demand3', thus enabling cells to increase rigidity under stress1,4-6. However, catch bonds are often weaker than slip bonds because they have cryptic binding sites that are usually buried7,8. Here we show that catch bonds render reconstituted cytoskeletal actin networks stronger than slip bonds, even though the individual bonds are weaker. Simulations show that slip bonds remain trapped in stress-free areas, whereas weak binding allows catch bonds to mitigate crack initiation by moving to high-tension areas. This 'dissociation on demand' explains how cells combine mechanical strength with the adaptability required for shape change, and is relevant to diseases where catch bonding is compromised7,9, including focal segmental glomerulosclerosis10 caused by the α-actinin-4 mutant studied here. We surmise that catch bonds are the key to create life-like materials.
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Affiliation(s)
- Yuval Mulla
- Living Matter Department, AMOLF, Amsterdam, The Netherlands
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Mario J Avellaneda
- Living Matter Department, AMOLF, Amsterdam, The Netherlands
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Antoine Roland
- Living Matter Department, AMOLF, Amsterdam, The Netherlands
| | - Lucia Baldauf
- Living Matter Department, AMOLF, Amsterdam, The Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands
| | - Wonyeong Jung
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Taeyoon Kim
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Sander J Tans
- Living Matter Department, AMOLF, Amsterdam, The Netherlands.
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
| | - Gijsje H Koenderink
- Living Matter Department, AMOLF, Amsterdam, The Netherlands.
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, The Netherlands.
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Dahal N, Sharma S, Phan B, Eis A, Popa I. Mechanical regulation of talin through binding and history-dependent unfolding. SCIENCE ADVANCES 2022; 8:eabl7719. [PMID: 35857491 DOI: 10.1126/sciadv.abl7719] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Talin is a force-sensing multidomain protein and a major player in cellular mechanotransduction. Here, we use single-molecule magnetic tweezers to investigate the mechanical response of the R8 rod domain of talin. We find that under various force cycles, the R8 domain of talin can display a memory-dependent behavior: At the same low force (<10 pN), the same protein molecule shows vastly different unfolding kinetics. This history-dependent behavior indicates the evolution of a unique force-induced native state. We measure through mechanical unfolding that talin R8 domain binds one of its ligands, DLC1, with much higher affinity than previously reported. This strong interaction can explain the antitumor response of DLC1 by regulating inside-out activation of integrins. Together, our results paint a complex picture for the mechanical unfolding of talin in the physiological range and a new mechanism of function of DLC1 to regulate inside-out activation of integrins.
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Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Binh Phan
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave., Milwaukee, WI 53211, USA
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Stirnemann G. Molecular interpretation of single-molecule force spectroscopy experiments with computational approaches. Chem Commun (Camb) 2022; 58:7110-7119. [PMID: 35678696 DOI: 10.1039/d2cc01350a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single molecule force-spectroscopy techniques have granted access to unprecedented molecular-scale details about biochemical and biological mechanisms. However, the interpretation of the experimental data is often challenging. Computational and simulation approaches (all-atom steered MD simulations in particular) are key to provide molecular details about the associated mechanisms, to help test different hypotheses and to predict experimental results. In this review, particular recent efforts directed towards the molecular interpretation of single-molecule force spectroscopy experiments on proteins and protein-related systems (often in close collaboration with experimental groups) will be presented. These results will be discussed in the broader context of the field, highlighting the recent achievements and the ongoing challenges for computational biophysicists and biochemists. In particular, I will focus on the input gained from molecular simulations approaches to rationalize the origin of the unfolded protein elasticity and the protein conformational behavior under force, to understand how force denaturation differs from chemical, thermal or shear unfolding, and to unravel the molecular details of unfolding events for a variety of systems. I will also discuss the use of models based on Langevin dynamics on a 1-D free-energy surface to understand the effect of protein segmentation on the work exerted by a force, or, at the other end of the spectrum of computational techniques, how quantum calculations can help to understand the reactivity of disulfide bridges exposed to force.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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The Power of Touch: Type 4 Pili, the von Willebrand A Domain, and Surface Sensing by Pseudomonas aeruginosa. J Bacteriol 2022; 204:e0008422. [PMID: 35612303 PMCID: PMC9210963 DOI: 10.1128/jb.00084-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Most microbes in the biosphere are attached to surfaces, where they experience mechanical forces due to hydrodynamic flow and cell-to-substratum interactions. These forces likely serve as mechanical cues that influence bacterial physiology and eventually drive environmental adaptation and fitness. Mechanosensors are cellular components capable of sensing a mechanical input and serve as part of a larger system for sensing and transducing mechanical signals. Two cellular components in bacteria that have emerged as candidate mechanosensors are the type IV pili (TFP) and the flagellum. Current models posit that bacteria transmit and convert TFP- and/or flagellum-dependent mechanical force inputs into biochemical signals, including cAMP and c-di-GMP, to drive surface adaptation. Here, we discuss the impact of force-induced changes on the structure and function of two eukaryotic proteins, titin and the human von Willebrand factor (vWF), and these proteins’ relevance to bacteria. Given the wealth of understanding about these eukaryotic mechanosensors, we can use them as a framework to understand the effect of force on Pseudomonas aeruginosa during the early stages of biofilm formation, with a particular emphasis on TFP and the documented surface-sensing mechanosensors PilY1 and FimH. We also discuss the importance of disulfide bonds in mediating force-induced conformational changes, which may modulate mechanosensing and downstream biochemical signaling. We conclude by sharing our perspective on the state of the field and what we deem exciting frontiers in studying bacterial mechanosensing to better understand the mechanisms whereby bacteria transition from a planktonic to a biofilm lifestyle.
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Nair AG, Perumalla DS, Anjukandi P. Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D. Phys Chem Chem Phys 2022; 24:7691-7699. [PMID: 35311864 DOI: 10.1039/d1cp05819c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N-terminal disulfide bond oxidoreductase-D (nDsbD), an essential redox enzyme in Gram-negative bacteria, consists of a single disulfide bond (Cys103-Cys109) in its active site. The enzymatic functions are believed to be regulated by an electron transfer mediated redox switching of the disulfide bond, which is vital in controlling bacterial virulence factors. In light of the disulfide bond's inclination towards nucleophilic cleavage, it is also plausible that an internal nucleophile could second the existing electron transfer mechanism in nDsbD. Using QM/MM MD metadynamics simulations, we explore different possibilities of generating an internal nucleophile near the nDsbD active site, which could serve as a fail-over mechanism in cleaving the disulfide bond. The simulations show the formation of the internal nucleophile Tyr42O- (F ≈ 9 kcal mol-1) and its stabilization through the solvent medium. The static gas-phase calculations show that Tyr42O- could be a potential nucleophile for cleaving the S-S bond. Most strikingly, it is also seen that Tyr42O- and Asp68OH communicate with each other through a proton-hole like water wire (F ≈ 12 kcal mol-1), thus modulating the nucleophile formation. Accordingly, we propose the role of a solvent in regulating the internal nucleophilic reactions and the subsequent self-activation of nDsbD. We believe that this could be deterministic while designing enzyme-targeted inhibitor compounds.
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Affiliation(s)
- Aparna G Nair
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
| | | | - Padmesh Anjukandi
- Department of Chemistry, Indian Institute of Technology, Palakkad-678557, Kerala, India.
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Sammon MS, Biewend M, Michael P, Schirra S, Ončák M, Binder WH, Beyer MK. Activation of a Copper Biscarbene Mechano-Catalyst Using Single-Molecule Force Spectroscopy Supported by Quantum Chemical Calculations. Chemistry 2021; 27:8723-8729. [PMID: 33822419 PMCID: PMC8251802 DOI: 10.1002/chem.202100555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Indexed: 11/17/2022]
Abstract
Single-molecule force spectroscopy allows investigation of the effect of mechanical force on individual bonds. By determining the forces necessary to sufficiently activate bonds to trigger dissociation, it is possible to predict the behavior of mechanophores. The force necessary to activate a copper biscarbene mechano-catalyst intended for self-healing materials was measured. By using a safety line bypassing the mechanophore, it was possible to pinpoint the dissociation of the investigated bond and determine rupture forces to range from 1.6 to 2.6 nN at room temperature in dimethyl sulfoxide. The average length-increase upon rupture of the Cu-C bond, due to the stretching of the safety line, agrees with quantum chemical calculations, but the values exhibit an unusual scattering. This scattering was assigned to the conformational flexibility of the mechanophore, which includes formation of a threaded structure and recoiling of the safety line.
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Affiliation(s)
- Matthew S. Sammon
- Institut für Ionenphysik und Angewandte PhysikUniversität InnsbruckTechnikerstraße 256020InnsbruckAustria
| | - Michel Biewend
- Department of Macromolecular ChemistryMartin-Luther-Universität Halle-Wittenbergvon-Danckelmann-Platz 406120Halle (Saale)Germany
| | - Philipp Michael
- Department of Macromolecular ChemistryMartin-Luther-Universität Halle-Wittenbergvon-Danckelmann-Platz 406120Halle (Saale)Germany
| | - Simone Schirra
- Institut für Ionenphysik und Angewandte PhysikUniversität InnsbruckTechnikerstraße 256020InnsbruckAustria
| | - Milan Ončák
- Institut für Ionenphysik und Angewandte PhysikUniversität InnsbruckTechnikerstraße 256020InnsbruckAustria
| | - Wolfgang H. Binder
- Department of Macromolecular ChemistryMartin-Luther-Universität Halle-Wittenbergvon-Danckelmann-Platz 406120Halle (Saale)Germany
| | - Martin K. Beyer
- Institut für Ionenphysik und Angewandte PhysikUniversität InnsbruckTechnikerstraße 256020InnsbruckAustria
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13
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Kadre D, Iyer BVS. Modeling Local Oscillatory Shear Dynamics of Functionalized Polymer Grafted Nanoparticles. MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202100005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Diksha Kadre
- Department of Chemical Engineering Indian Institute of Technology Hyderabad 502285 India
| | - Balaji V. S. Iyer
- Department of Chemical Engineering Indian Institute of Technology Hyderabad 502285 India
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14
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Hao X, Zhang J, Yang Y, Wang H, Chi Q. Single‐Molecule Interactions between Heme Proteins and Carboxylic Groups in Various Chemical Environments. ChemElectroChem 2020. [DOI: 10.1002/celc.202001234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xian Hao
- School of Public Health & Jiangxi Provincial Key Laboratory of Preventive Medicine Nanchang University, Nanchang Jiangxi 330006 China
| | - Jingdong Zhang
- Department of Chemistry Technical University of Denmark 2800 Kgs. Lyngby Denmark
| | - Yifei Yang
- School of Public Health & Jiangxi Provincial Key Laboratory of Preventive Medicine Nanchang University, Nanchang Jiangxi 330006 China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry Research Center of Biomembranomics Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 China
| | - Qijin Chi
- Department of Chemistry Technical University of Denmark 2800 Kgs. Lyngby Denmark
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15
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Affiliation(s)
- Guillaume De Bo
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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16
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Three concomitant C–C dissociation pathways during the mechanical activation of an N-heterocyclic carbene precursor. Nat Chem 2020; 12:826-831. [DOI: 10.1038/s41557-020-0509-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 06/12/2020] [Indexed: 11/09/2022]
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17
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Gao Y, Zhou D, Lyu J, A S, Xu Q, Newland B, Matyjaszewski K, Tai H, Wang W. Complex polymer architectures through free-radical polymerization of multivinyl monomers. Nat Rev Chem 2020; 4:194-212. [PMID: 37128047 DOI: 10.1038/s41570-020-0170-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2020] [Indexed: 01/26/2023]
Abstract
The construction of complex polymer architectures with well-defined topology, composition and functionality has been extensively explored as the molecular basis for the development of modern polymer materials. The unique reaction kinetics of free-radical polymerization leads to the concurrent formation of crosslinks between polymer chains and rings within an individual chain and, thus, free-radical (co)polymerization of multivinyl monomers provides a facile method to manipulate chain topology and functionality. Regulating the relative contribution of these intermolecular and intramolecular chain-propagation reactions is the key to the construction of architecturally complex polymers. This can be achieved through the design of new monomers or by spatially or kinetically controlling crosslinking reactions. These mechanisms enable the synthesis of various polymer architectures, including linear, cyclized, branched and star polymer chains, as well as crosslinked networks. In this Review, we highlight some of the contemporary experimental strategies to prepare complex polymer architectures using radical polymerization of multivinyl monomers. We also examine the recent development of characterization techniques for sub-chain connections in such complex macromolecules. Finally, we discuss how these crosslinking reactions have been engineered to generate advanced polymer materials for use in a variety of biomedical applications.
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Ni J, Ren X, Zheng J. Friction and Wear Mechanism Analysis of Polymer Flexible Cable Using a High Natural Frequency Piezoelectric Sensor. SENSORS 2020; 20:s20041044. [PMID: 32075176 PMCID: PMC7070635 DOI: 10.3390/s20041044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 11/16/2022]
Abstract
The friction and wear of flexible cables are the main factors that cause electrical breakdown and insulation aging, and they greatly reduce the reliability and safety of robots. In order to enhance the reliability and safety of the robot, it is of great necessity to investigate the friction and wear mechanisms of the flexible cable. In this research, the friction and wear mechanisms have been discussed. The effects of relative speed, ambient temperature, and positive pressure on the flexible cables are considered by an orthogonal frictional movement. The cable friction force has been measured by a piezoelectric sensor with high natural frequency characteristics. The relations among friction and different factors affecting friction have also been discussed. The results show that the relative speed and the ambient temperature are the main factors affecting the friction and wear of the cable; the main form of flexible cable wear is mechanical-force chemical friction and wear. Those discoveries will greatly deepen the understanding of the friction and wear mechanisms of flexible cables, and will be beneficial to robot cable-reliability design.
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19
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Dopieralski P, Zoloff Michoff ME, Marx D. Mechanochemical disulfide reduction reveals imprints of noncovalent sulfur⋯oxygen chalcogen bonds in protein-inspired mimics in aqueous solution. Phys Chem Chem Phys 2020; 22:25112-25117. [DOI: 10.1039/d0cp04026f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chalcogen bonds in proteins are found to impact on the mechanochemical reduction of disulfide bridges in aqueous environments.
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Affiliation(s)
| | | | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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20
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Ma Z, Yang P, Zhang X, Jiang K, Song Y, Zhang W. Quantifying the Chain Folding in Polymer Single Crystals by Single-Molecule Force Spectroscopy. ACS Macro Lett 2019; 8:1194-1199. [PMID: 35619456 DOI: 10.1021/acsmacrolett.9b00607] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chain folding is a motif of polymer crystallization, which is essential for determining the crystallization kinetics. However, the experimental quantification of the chain folding remains a challenge because of limited instrumental resolution. Here, we quantify chain folding in solution-grown single crystals by using atomic force microscopy (AFM)-based single-molecule force spectroscopy. The fingerprint spectrum of force-induced chain motion allows us to decipher the adjacent and nonadjacent re-entry folding with spatial resolution of subnanometers. The average fractions of adjacent re-entry folds ⟨f⟩ are in the range 91-95% for polycaprolactone, poly-l-lactic acid, and polyamide 66, which is higher than the values determined by other classical technologies. The established single-molecule method is applicable to a broad range of crystalline polymer systems with different chain conformations or compositions.
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Affiliation(s)
- Ziwen Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Peng Yang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Xiaoye Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Ke Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Yu Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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21
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Yuan G, Ma Q, Wu T, Wang M, Li X, Zuo J, Zheng P. Multistep Protein Unfolding Scenarios from the Rupture of a Complex Metal Cluster Cd 3S 9. Sci Rep 2019; 9:10518. [PMID: 31324867 PMCID: PMC6642161 DOI: 10.1038/s41598-019-47004-y] [Citation(s) in RCA: 10] [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: 03/15/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
Protein (un)folding is a complex and essential process. With the rapid development of single-molecule techniques, we can detect multiple and transient proteins (un)folding pathways/intermediates. However, the observation of multiple multistep (>2) unfolding scenarios for a single protein domain remains limited. Here, we chose metalloprotein with relatively stable and multiple metal-ligand coordination bonds as a system for such a purpose. Using AFM-based single-molecule force spectroscopy (SMFS), we successfully demonstrated the complex and multistep protein unfolding scenarios of the β-domain of a human protein metallothionein-3 (MT). MT is a protein of ~60 amino acids (aa) in length with 20 cysteines for various metal binding, and the β-domain (βMT) is of ~30 aa with an M3S9 metal cluster. We detected four different types of three-step protein unfolding scenarios from the Cd-βMT, which can be possibly explained by the rupture of Cd-S bonds in the complex Cd3S9 metal cluster. In addition, complex unfolding scenarios with four rupture peaks were observed. The Cd-S bonds ruptured in both single bond and multiple bonds modes. Our results provide not only evidence for multistep protein unfolding phenomena but also reveal unique properties of metalloprotein system using single-molecule AFM.
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Affiliation(s)
- Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Qun Ma
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Mengdi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Jinglin Zuo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China.
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22
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Pill MF, East ALL, Marx D, Beyer MK, Clausen‐Schaumann H. Mechanical Activation Drastically Accelerates Amide Bond Hydrolysis, Matching Enzyme Activity. Angew Chem Int Ed Engl 2019; 58:9787-9790. [DOI: 10.1002/anie.201902752] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/10/2019] [Indexed: 01/21/2023]
Affiliation(s)
- Michael F. Pill
- Department of Applied Sciences and MechatronicsMunich University of Applied Sciences Lothstrasse 34 80334 Munich Germany
- Center for Nanoscience (CeNS) Schellingstrasse 4 80799 Munich Germany
| | - Allan L. L. East
- Department of Chemistry and BiochemistryUniversity of Regina Regina SK S4S0A2 Canada
| | - Dominik Marx
- Lehrstuhl für Theoretische ChemieRuhr-Universität Bochum 44780 Bochum Germany
| | - Martin K. Beyer
- Institut für Ionenphysik und Angewandte PhysikUniversität Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
| | - Hauke Clausen‐Schaumann
- Department of Applied Sciences and MechatronicsMunich University of Applied Sciences Lothstrasse 34 80334 Munich Germany
- Center for Nanoscience (CeNS) Schellingstrasse 4 80799 Munich Germany
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23
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Pill MF, East ALL, Marx D, Beyer MK, Clausen‐Schaumann H. Mechanische Aktivierung beschleunigt die Hydrolyse der Amidbindung drastisch, vergleichbar der Aktivität von Enzymen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Michael F. Pill
- Fakultät für angewandte Naturwissenschaften und MechatronikHochschule für angewandte Wissenschaften München Lothstraße 34 80334 München Deutschland
- Center for Nanoscience (CeNS) Schellingstraße 4 80799 München Deutschland
| | - Allan L. L. East
- Department of Chemistry and BiochemistryUniversity of Regina Regina SK S4S0A2 Kanada
| | - Dominik Marx
- Lehrstuhl für Theoretische ChemieRuhr-Universität Bochum 44780 Bochum Deutschland
| | - Martin K. Beyer
- Institut für Ionenphysik und Angewandte PhysikUniversität Innsbruck Technikerstraße 25 6020 Innsbruck Österreich
| | - Hauke Clausen‐Schaumann
- Fakultät für angewandte Naturwissenschaften und MechatronikHochschule für angewandte Wissenschaften München Lothstraße 34 80334 München Deutschland
- Center for Nanoscience (CeNS) Schellingstraße 4 80799 München Deutschland
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24
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Kulik HJ. MODELING MECHANOCHEMISTRY FROM FIRST PRINCIPLES. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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Beedle AEM, Mora M, Davis CT, Snijders AP, Stirnemann G, Garcia-Manyes S. Forcing the reversibility of a mechanochemical reaction. Nat Commun 2018; 9:3155. [PMID: 30089863 PMCID: PMC6082871 DOI: 10.1038/s41467-018-05115-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/13/2018] [Indexed: 11/09/2022] Open
Abstract
Mechanical force modifies the free-energy surface of chemical reactions, often enabling thermodynamically unfavoured reaction pathways. Most of our molecular understanding of force-induced reactivity is restricted to the irreversible homolytic scission of covalent bonds and ring-opening in polymer mechanophores. Whether mechanical force can by-pass thermodynamically locked reactivity in heterolytic bimolecular reactions and how this impacts the reaction reversibility remains poorly understood. Using single-molecule force-clamp spectroscopy, here we show that mechanical force promotes the thermodynamically disfavored SN2 cleavage of an individual protein disulfide bond by poor nucleophilic organic thiols. Upon force removal, the transition from the resulting high-energy unstable mixed disulfide product back to the initial, low-energy disulfide bond reactant becomes suddenly spontaneous, rendering the reaction fully reversible. By rationally varying the nucleophilicity of a series of small thiols, we demonstrate how force-regulated chemical kinetics can be finely coupled with thermodynamics to predict and modulate the reversibility of bimolecular mechanochemical reactions.
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Affiliation(s)
- Amy E M Beedle
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Marc Mora
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK
| | - Colin T Davis
- The Francis Crick Institute, Protein analysis and Proteomics Science Technology Platform, 1 Midland Road, London, NW1 1AT, UK
| | - Ambrosius P Snijders
- The Francis Crick Institute, Protein analysis and Proteomics Science Technology Platform, 1 Midland Road, London, NW1 1AT, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics, King's College London, London, WC2R 2LS, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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26
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Schönfelder J, Alonso-Caballero A, De Sancho D, Perez-Jimenez R. The life of proteins under mechanical force. Chem Soc Rev 2018; 47:3558-3573. [PMID: 29473060 DOI: 10.1039/c7cs00820a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Although much of our understanding of protein folding comes from studies of isolated protein domains in bulk, in the cellular environment the intervention of external molecular machines is essential during the protein life cycle. During the past decade single molecule force spectroscopy techniques have been extremely useful to deepen our understanding of these interventional molecular processes, as they allow for monitoring and manipulating mechanochemical events in individual protein molecules. Here, we review some of the critical steps in the protein life cycle, starting with the biosynthesis of the nascent polypeptide chain in the ribosome, continuing with the folding supported by chaperones and the translocation into different cell compartments, and ending with proteolysis in the proteasome. Along these steps, proteins experience molecular forces often combined with chemical transformations, affecting their folding and structure, which are measured or mimicked in the laboratory by the application of force with a single molecule apparatus. These mechanochemical reactions can potentially be used as targets for fighting against diseases. Inspired by these insightful experiments, we devise an outlook on the emerging field of mechanopharmacology, which reflects an alternative paradigm for drug design.
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27
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Hamlin TA, Swart M, Bickelhaupt FM. Nucleophilic Substitution (S N 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent. Chemphyschem 2018; 19:1315-1330. [PMID: 29542853 PMCID: PMC6001448 DOI: 10.1002/cphc.201701363] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 11/12/2022]
Abstract
The reaction potential energy surface (PES), and thus the mechanism of bimolecular nucleophilic substitution (SN 2), depends profoundly on the nature of the nucleophile and leaving group, but also on the central, electrophilic atom, its substituents, as well as on the medium in which the reaction takes place. Here, we provide an overview of recent studies and demonstrate how changes in any one of the aforementioned factors affect the SN 2 mechanism. One of the most striking effects is the transition from a double-well to a single-well PES when the central atom is changed from a second-period (e. g. carbon) to a higher-period element (e.g, silicon, germanium). Variations in nucleophilicity, leaving group ability, and bulky substituents around a second-row element central atom can then be exploited to change the single-well PES back into a double-well. Reversely, these variations can also be used to produce a single-well PES for second-period elements, for example, a stable pentavalent carbon species.
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Affiliation(s)
- Trevor A. Hamlin
- Department of Theoretical Chemistry andAmsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - Marcel Swart
- Department of Theoretical Chemistry andAmsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institut de Química Computacional I Catàlisi and Department de QuímicaUniversitat de Girona17003GironaSpain
- ICREAPg. Lluís Companys 2308010BarcelonaSpain
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry andAmsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute of Molecules and Materials (IMM)Radboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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28
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29
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Pijning AE, Chiu J, Yeo RX, Wong JWH, Hogg PJ. Identification of allosteric disulfides from labile bonds in X-ray structures. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171058. [PMID: 29515832 PMCID: PMC5830721 DOI: 10.1098/rsos.171058] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/03/2018] [Indexed: 05/08/2023]
Abstract
Protein disulfide bonds link pairs of cysteine sulfur atoms and are either structural or functional motifs. The allosteric disulfides control the function of the protein in which they reside when cleaved or formed. Here, we identify potential allosteric disulfides in all Protein Data Bank X-ray structures from bonds that are present in some molecules of a protein crystal but absent in others, or present in some structures of a protein but absent in others. We reasoned that the labile nature of these disulfides signifies a propensity for cleavage and so possible allosteric regulation of the protein in which the bond resides. A total of 511 labile disulfide bonds were identified. The labile disulfides are more stressed than the average bond, being characterized by high average torsional strain and stretching of the sulfur-sulfur bond and neighbouring bond angles. This pre-stress likely underpins their susceptibility to cleavage. The coagulation, complement and oxygen-sensing hypoxia inducible factor-1 pathways, which are known or have been suggested to be regulated by allosteric disulfides, are enriched in proteins containing labile disulfides. The identification of labile disulfide bonds will facilitate the study of this post-translational modification.
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Affiliation(s)
- Aster E. Pijning
- The Centenary Institute, Camperdown, New South Wales 2050, Australia
| | - Joyce Chiu
- The Centenary Institute, Camperdown, New South Wales 2050, Australia
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Reichelle X. Yeo
- The Centenary Institute, Camperdown, New South Wales 2050, Australia
| | - Jason W. H. Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Philip J. Hogg
- The Centenary Institute, Camperdown, New South Wales 2050, Australia
- National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, New South Wales 2006, Australia
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30
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Zhang T, Mbanga BL, Yashin VV, Balazs AC. Tailoring the mechanical properties of nanoparticle networks that encompass biomimetic catch bonds. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/polb.24542] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tao Zhang
- Department of Chemical EngineeringUniversity of PittsburghPittsburgh Pennsylvania 15261
| | - Badel L. Mbanga
- Department of Chemical EngineeringUniversity of PittsburghPittsburgh Pennsylvania 15261
| | - Victor V. Yashin
- Department of Chemical EngineeringUniversity of PittsburghPittsburgh Pennsylvania 15261
| | - Anna C. Balazs
- Department of Chemical EngineeringUniversity of PittsburghPittsburgh Pennsylvania 15261
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31
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32
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Stevenson R, De Bo G. Controlling Reactivity by Geometry in Retro-Diels–Alder Reactions under Tension. J Am Chem Soc 2017; 139:16768-16771. [DOI: 10.1021/jacs.7b08895] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Richard Stevenson
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Guillaume De Bo
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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33
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Beedle AEM, Mora M, Lynham S, Stirnemann G, Garcia-Manyes S. Tailoring protein nanomechanics with chemical reactivity. Nat Commun 2017; 8:15658. [PMID: 28585528 PMCID: PMC5467162 DOI: 10.1038/ncomms15658] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 04/13/2017] [Indexed: 12/22/2022] Open
Abstract
The nanomechanical properties of elastomeric proteins determine the elasticity of a variety of tissues. A widespread natural tactic to regulate protein extensibility lies in the presence of covalent disulfide bonds, which significantly enhance protein stiffness. The prevalent in vivo strategy to form disulfide bonds requires the presence of dedicated enzymes. Here we propose an alternative chemical route to promote non-enzymatic oxidative protein folding via disulfide isomerization based on naturally occurring small molecules. Using single-molecule force-clamp spectroscopy, supported by DFT calculations and mass spectrometry measurements, we demonstrate that subtle changes in the chemical structure of a transient mixed-disulfide intermediate adduct between a protein cysteine and an attacking low molecular-weight thiol have a dramatic effect on the protein's mechanical stability. This approach provides a general tool to rationalize the dynamics of S-thiolation and its role in modulating protein nanomechanics, offering molecular insights on how chemical reactivity regulates protein elasticity. Post-translational modifications modulate nanomechanics of proteins. Here the authors use single-molecule force-clamp spectroscopy supported by density functional theory calculations to show how reactive low-weight molecular thiol compounds directly affect mechanical protein folding.
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Affiliation(s)
- Amy E M Beedle
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
| | - Marc Mora
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
| | - Steven Lynham
- Centre of Excellence for Mass Spectrometry, King's College London, SE5 8AF London, UK
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Univ. Paris Denis Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, WC2R 2LS London, UK
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34
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Valentini A, Rivero D, Zapata F, García-Iriepa C, Marazzi M, Palmeiro R, Fdez. Galván I, Sampedro D, Olivucci M, Frutos LM. Optomechanical Control of Quantum Yield in Trans
-Cis
Ultrafast Photoisomerization of a Retinal Chromophore Model. Angew Chem Int Ed Engl 2017; 56:3842-3846. [DOI: 10.1002/anie.201611265] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/12/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Alessio Valentini
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
- Department of Biotechnology; Chemistry and Pharmacy; University of Siena; via A. Moro 2 53100 Siena Italy
| | - Daniel Rivero
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Felipe Zapata
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Cristina García-Iriepa
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
- Departamento de Química; Centro de Investigación en Síntesis Química (CISQ); University of La Rioja; Madre de Dios, 53 26006 Logroño Spain
| | - Marco Marazzi
- Theory-Modeling-Simulation SRSMC; Université de Lorraine-Nancy; Vandoeuvre-lès-Nancy, Nancy France
- Theory-Modeling-Simulation SRSMC; CNRS; SRSMC Boulevard des Aiguillettes Vandoeuvre-lès-Nancy France
| | - Raúl Palmeiro
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Ignacio Fdez. Galván
- Department of Chemistry-Ångström; Uppsala Center for Computational Chemistry-UC 3; Uppsala University; Box 518 75120 Uppsala Sweden
| | - Diego Sampedro
- Departamento de Química; Centro de Investigación en Síntesis Química (CISQ); University of La Rioja; Madre de Dios, 53 26006 Logroño Spain
| | - Massimo Olivucci
- Department of Biotechnology; Chemistry and Pharmacy; University of Siena; via A. Moro 2 53100 Siena Italy
- Department of Chemistry; Bowling Green State University; Bowling Green OH 43403 USA
- USIAS and Institut de Physique et Chimie des Matériaux de Strasbourg; Université de Strasbourg-CNRS; 67034 Strasbourg France
| | - Luis Manuel Frutos
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
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35
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Valentini A, Rivero D, Zapata F, García-Iriepa C, Marazzi M, Palmeiro R, Fdez. Galván I, Sampedro D, Olivucci M, Frutos LM. Optomechanical Control of Quantum Yield in Trans
-Cis
Ultrafast Photoisomerization of a Retinal Chromophore Model. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alessio Valentini
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
- Department of Biotechnology; Chemistry and Pharmacy; University of Siena; via A. Moro 2 53100 Siena Italy
| | - Daniel Rivero
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Felipe Zapata
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Cristina García-Iriepa
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
- Departamento de Química; Centro de Investigación en Síntesis Química (CISQ); University of La Rioja; Madre de Dios, 53 26006 Logroño Spain
| | - Marco Marazzi
- Theory-Modeling-Simulation SRSMC; Université de Lorraine-Nancy; Vandoeuvre-lès-Nancy, Nancy France
- Theory-Modeling-Simulation SRSMC; CNRS; SRSMC Boulevard des Aiguillettes Vandoeuvre-lès-Nancy France
| | - Raúl Palmeiro
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Ignacio Fdez. Galván
- Department of Chemistry-Ångström; Uppsala Center for Computational Chemistry-UC 3; Uppsala University; Box 518 75120 Uppsala Sweden
| | - Diego Sampedro
- Departamento de Química; Centro de Investigación en Síntesis Química (CISQ); University of La Rioja; Madre de Dios, 53 26006 Logroño Spain
| | - Massimo Olivucci
- Department of Biotechnology; Chemistry and Pharmacy; University of Siena; via A. Moro 2 53100 Siena Italy
- Department of Chemistry; Bowling Green State University; Bowling Green OH 43403 USA
- USIAS and Institut de Physique et Chimie des Matériaux de Strasbourg; Université de Strasbourg-CNRS; 67034 Strasbourg France
| | - Luis Manuel Frutos
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
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36
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Lei H, Guo Y, Hu X, Hu C, Hu X, Li H. Reversible Unfolding and Folding of the Metalloprotein Ferredoxin Revealed by Single-Molecule Atomic Force Microscopy. J Am Chem Soc 2017; 139:1538-1544. [DOI: 10.1021/jacs.6b11371] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hai Lei
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Yabin Guo
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Xiaodong Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Chunguang Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xiaotang Hu
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Hongbin Li
- State
Key Laboratory of Precision Measurements Technology and Instruments,
School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
- Department
of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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37
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Dopieralski P, Ribas–Arino J, Anjukandi P, Krupicka M, Marx D. Unexpected mechanochemical complexity in the mechanistic scenarios of disulfide bond reduction in alkaline solution. Nat Chem 2016; 9:164-170. [DOI: 10.1038/nchem.2632] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/17/2016] [Indexed: 01/14/2023]
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38
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Beedle AEM, Lynham S, Garcia-Manyes S. Protein S-sulfenylation is a fleeting molecular switch that regulates non-enzymatic oxidative folding. Nat Commun 2016; 7:12490. [PMID: 27546612 PMCID: PMC4996944 DOI: 10.1038/ncomms12490] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/08/2016] [Indexed: 12/31/2022] Open
Abstract
The post-translational modification S-sulfenylation functions as a key sensor of oxidative stress. Yet the dynamics of sulfenic acid in proteins remains largely elusive due to its fleeting nature. Here we use single-molecule force-clamp spectroscopy and mass spectrometry to directly capture the reactivity of an individual sulfenic acid embedded within the core of a single Ig domain of the titin protein. Our results demonstrate that sulfenic acid is a crucial short-lived intermediate that dictates the protein's fate in a conformation-dependent manner. When exposed to the solution, sulfenic acid rapidly undergoes further chemical modification, leading to irreversible protein misfolding; when cryptic in the protein's microenvironment, it readily condenses with a neighbouring thiol to create a protective disulfide bond, which assists the functional folding of the protein. This mechanism for non-enzymatic oxidative folding provides a plausible explanation for redox-modulated stiffness of proteins that are physiologically exposed to mechanical forces, such as cardiac titin. Protein S-sulfenylation is a posttranslational modification that can act as a sensor of redox oxidative stress. Here the authors show that, following mechanical unfolding, sulfenic acid drives disulfide bond reformation and guides non-enzymatic oxidative folding.
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Affiliation(s)
- Amy E M Beedle
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Steven Lynham
- Centre of Excellence for Mass Spectrometry, King's College London, London SE5 8AF, UK
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
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39
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Pill MF, Holz K, Preußke N, Berger F, Clausen-Schaumann H, Lüning U, Beyer MK. Mechanochemical Cycloreversion of Cyclobutane Observed at the Single Molecule Level. Chemistry 2016; 22:12034-9. [PMID: 27415146 DOI: 10.1002/chem.201600866] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Indexed: 11/12/2022]
Abstract
Mechanochemical cycloreversion of cyclobutane is known from ultrasound experiments. It is, however, not clear which forces are required to induce the cycloreversion. In atomic force microscopy (AFM) experiments, on the other hand, it is notoriously difficult to assign the ruptured bond. We have solved this problem through the synthesis of tailored macrocycles, in which the cyclobutane mechanophore is bypassed by an ethylene glycol chain of specific length. This macrocycle is covalently anchored between a glass substrate and an AFM cantilever by polyethylene glycol linkers. Upon mechanical stretching of the macrocycle, cycloreversion occurs, which is identified by a defined length increase of the stretched polymer. The measured length change agrees with the value calculated with the external force explicitly included (EFEI) method. By using two different lengths for the ethylene glycol safety line, the assignment becomes unambiguous. Mechanochemical cycloreversion of cyclobutane is observed at forces above 1.7 nN.
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Affiliation(s)
- Michael F Pill
- Department of Applied Natural Sciences and Mechatronics, Munich University of Applied Sciences, Lothstraße 34, 80335, Munich, Germany.,Center for Nanoscience (CeNS), Geschwister-Scholl-Platz 1, Munich, Germany
| | - Katharina Holz
- Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098, Kiel, Germany
| | - Nils Preußke
- Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098, Kiel, Germany
| | - Florian Berger
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens-Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Hauke Clausen-Schaumann
- Department of Applied Natural Sciences and Mechatronics, Munich University of Applied Sciences, Lothstraße 34, 80335, Munich, Germany.,Center for Nanoscience (CeNS), Geschwister-Scholl-Platz 1, Munich, Germany
| | - Ulrich Lüning
- Otto-Diels-Institut für Organische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098, Kiel, Germany.
| | - Martin K Beyer
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens-Universität Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
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40
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Roy M, Grazioli G, Andricioaei I. Rate turnover in mechano-catalytic coupling: A model and its microscopic origin. J Chem Phys 2016; 143:045105. [PMID: 26233168 DOI: 10.1063/1.4926664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A novel aspect in the area of mechano-chemistry concerns the effect of external forces on enzyme activity, i.e., the existence of mechano-catalytic coupling. Recent experiments on enzyme-catalyzed disulphide bond reduction in proteins under the effect of a force applied on the termini of the protein substrate reveal an unexpected biphasic force dependence for the bond cleavage rate. Here, using atomistic molecular dynamics simulations combined with Smoluchowski theory, we propose a model for this behavior. For a broad range of forces and systems, the model reproduces the experimentally observed rates by solving a reaction-diffusion equation for a "protein coordinate" diffusing in a force-dependent effective potential. The atomistic simulations are used to compute, from first principles, the parameters of the model via a quasiharmonic analysis. Additionally, the simulations are also used to provide details about the microscopic degrees of freedom that are important for the underlying mechano-catalysis.
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Affiliation(s)
- Mahua Roy
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - Gianmarc Grazioli
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, California 92697, USA
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41
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Mbanga BL, Iyer BVS, Yashin VV, Balazs AC. Tuning the Mechanical Properties of Polymer-Grafted Nanoparticle Networks through the Use of Biomimetic Catch Bonds. Macromolecules 2016. [DOI: 10.1021/acs.macromol.5b02455] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Badel L. Mbanga
- Chemical
Engineering Department, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Balaji V. S. Iyer
- Department
of Chemical Engineering, Indian Institute of Technology, Hyderabad, India
| | - Victor V. Yashin
- Chemical
Engineering Department, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Anna C. Balazs
- Chemical
Engineering Department, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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42
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Dopieralski P, Ribas-Arino J, Anjukandi P, Krupicka M, Marx D. Force-Induced Reversal of β-Eliminations: Stressed Disulfide Bonds in Alkaline Solution. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Przemyslaw Dopieralski
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
- Faculty of Chemistry; University of Wroclaw; Joliot-Curie 14 50-383 Wroclaw Poland
| | - Jordi Ribas-Arino
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
- Departament de Química Física and IQTCUB; Universitat de Barcelona; Av. Diagonal 645 08028 Barcelona Spain
| | - Padmesh Anjukandi
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
| | - Martin Krupicka
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
- Max-Planck-Institut für Chemische Energiekonversion; Stiftstrasse 34-36 45470 Mülheim an der Ruhr Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie; Ruhr-Universität Bochum; 44780 Bochum Germany
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43
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Dopieralski P, Ribas-Arino J, Anjukandi P, Krupicka M, Marx D. Force-Induced Reversal of β-Eliminations: Stressed Disulfide Bonds in Alkaline Solution. Angew Chem Int Ed Engl 2015; 55:1304-8. [PMID: 26634891 DOI: 10.1002/anie.201508005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/04/2015] [Indexed: 12/17/2022]
Abstract
Understanding the impact of tensile forces on disulfide bond cleavage is not only crucial to the breaking of cross-linkers in vulcanized materials such as strained rubber, but also to the regulation of protein activity by disulfide switches. By using ab initio simulations in the condensed phase, we investigated the response of disulfide cleavage by β-elimination to mechanical stress. We reveal that the rate-determining first step of the thermal reaction, which is the abstraction of the β-proton, is insensitive to external forces. However, forces larger than about 1 nN were found to reshape the free-energy landscape of the reaction so dramatically that a second channel is created, where the order of the reaction steps is reversed, turning β-deprotonation into a barrier-free follow-up process to C-S cleavage. This transforms a slow and force-independent process with second-order kinetics into a unimolecular reaction that is greatly accelerated by mechanical forces.
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Affiliation(s)
- Przemyslaw Dopieralski
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany. .,Faculty of Chemistry, University of Wroclaw, Joliot-Curie 14, 50-383, Wroclaw, Poland.
| | - Jordi Ribas-Arino
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany. .,Departament de Química Física and IQTCUB, Universitat de Barcelona, Av. Diagonal 645, 08028, Barcelona, Spain.
| | - Padmesh Anjukandi
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany
| | - Martin Krupicka
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany.,Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780, Bochum, Germany.
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44
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Abstract
Zinc fingers are highly ubiquitous structural motifs that provide stability to proteins, thus contributing to their correct folding. Despite the high thermodynamic stability of the ZnCys4 centers, their kinetic properties display remarkable lability. Here, we use a combination of protein engineering with single molecule force spectroscopy atomic force microscopy (AFM) to uncover the surprising mechanical lability (∼90 pN) of the individual Zn-S bonds that form the two equivalent zinc finger motifs embedded in the structure of the multidomain DnaJ chaperone. Rational mutations within the zinc coordinating residues enable direct identification of the chemical determinants that regulate the interplay between zinc binding-requiring the presence of all four cysteines-and disulfide bond formation. Finally, our observations show that binding to hydrophobic short peptides drastically increases the mechanical stability of DnaJ. Altogether, our experimental approach offers a detailed, atomistic vista on the fine chemical mechanisms that govern the nanomechanics of individual, naturally occurring zinc finger.
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Affiliation(s)
- Judit Perales-Calvo
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London , Strand, WC2R 2LS, London, United Kingdom
| | - Ainhoa Lezamiz
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London , Strand, WC2R 2LS, London, United Kingdom
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London , Strand, WC2R 2LS, London, United Kingdom
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45
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Beedle AEM, Lezamiz A, Stirnemann G, Garcia-Manyes S. The mechanochemistry of copper reports on the directionality of unfolding in model cupredoxin proteins. Nat Commun 2015; 6:7894. [PMID: 26235284 PMCID: PMC4532836 DOI: 10.1038/ncomms8894] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/24/2015] [Indexed: 11/09/2022] Open
Abstract
Understanding the directionality and sequence of protein unfolding is crucial to elucidate the underlying folding free energy landscape. An extra layer of complexity is added in metalloproteins, where a metal cofactor participates in the correct, functional fold of the protein. However, the precise mechanisms by which organometallic interactions are dynamically broken and reformed on (un)folding are largely unknown. Here we use single molecule force spectroscopy AFM combined with protein engineering and MD simulations to study the individual unfolding pathways of the blue-copper proteins azurin and plastocyanin. Using the nanomechanical properties of the native copper centre as a structurally embedded molecular reporter, we demonstrate that both proteins unfold via two independent, competing pathways. Our results provide experimental evidence of a novel kinetic partitioning scenario whereby the protein can stochastically unfold through two distinct main transition states placed at the N and C termini that dictate the direction in which unfolding occurs.
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Affiliation(s)
- Amy E M Beedle
- Department of Physics, King's College London, London WC2R 2LS, UK
| | - Ainhoa Lezamiz
- Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Guillaume Stirnemann
- CNRS - Institut de Biologie Physico-Chimique - PSL Research University, Laboratoire de Biochimie Théorique, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics, King's College London, London WC2R 2LS, UK.,Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
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46
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Rivero D, Valentini A, Fernández-González MÁ, Zapata F, García-Iriepa C, Sampedro D, Palmeiro R, Frutos LM. Mechanical Forces Alter Conical Intersections Topology. J Chem Theory Comput 2015; 11:3740-5. [DOI: 10.1021/acs.jctc.5b00375] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Rivero
- Química
Física, Universidad de Alcalá, E- 28871 Alcalá de Henares, Madrid, Spain
| | - Alessio Valentini
- Química
Física, Universidad de Alcalá, E- 28871 Alcalá de Henares, Madrid, Spain
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | - Felipe Zapata
- Química
Física, Universidad de Alcalá, E- 28871 Alcalá de Henares, Madrid, Spain
| | - Cristina García-Iriepa
- Química
Física, Universidad de Alcalá, E- 28871 Alcalá de Henares, Madrid, Spain
- Departamento
de Química, Centro de Investigación en Síntesis Química (CISQ), Madre de Dios, 51, E-26006, Logroño, Spain
| | - Diego Sampedro
- Departamento
de Química, Centro de Investigación en Síntesis Química (CISQ), Madre de Dios, 51, E-26006, Logroño, Spain
| | - Raúl Palmeiro
- Química
Física, Universidad de Alcalá, E- 28871 Alcalá de Henares, Madrid, Spain
| | - Luis Manuel Frutos
- Química
Física, Universidad de Alcalá, E- 28871 Alcalá de Henares, Madrid, Spain
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47
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Iyer BV, Yashin VV, Balazs AC. Harnessing biomimetic catch bonds to create mechanically robust nanoparticle networks. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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48
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Zheng P, Arantes GM, Field MJ, Li H. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule. Nat Commun 2015; 6:7569. [PMID: 26108369 PMCID: PMC4491811 DOI: 10.1038/ncomms8569] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/19/2015] [Indexed: 02/06/2023] Open
Abstract
Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions. The investigation of the chemical reactivity of metal centres in metalloproteins in aqueous solution is challenging. Here, the authors demonstrate the use of single molecule force spectroscopy to study the chemical reactivity of the iron-sulfur centre in rubredoxin in aqueous solution.
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Affiliation(s)
- Peng Zheng
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1.,School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210063, P. R. China
| | - Guilherme M Arantes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenue Lineu Prestes 748, São Paulo SP 05508-900, Brazil
| | - Martin J Field
- Institut de Biologie Structurale (IBS) Jean-Pierre Ebel, CEA/CNRS/Universite Joseph Fourier, 71 Avenue des Martyrs, CS 10090, Grenoble 9 38044, France
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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49
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Cao P, Yoon G, Tao W, Eom K, Park HS. The role of binding site on the mechanical unfolding mechanism of ubiquitin. Sci Rep 2015; 5:8757. [PMID: 25736913 PMCID: PMC4348633 DOI: 10.1038/srep08757] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 02/03/2015] [Indexed: 12/16/2022] Open
Abstract
We apply novel atomistic simulations based on potential energy surface exploration to investigate the constant force-induced unfolding of ubiquitin. At the experimentally-studied force clamping level of 100 pN, we find a new unfolding mechanism starting with the detachment between β5 and β3 involving the binding site of ubiquitin, the Ile44 residue. This new unfolding pathway leads to the discovery of new intermediate configurations, which correspond to the end-to-end extensions previously seen experimentally. More importantly, it demonstrates the novel finding that the binding site of ubiquitin can be responsible not only for its biological functions, but also its unfolding dynamics. We also report in contrast to previous single molecule constant force experiments that when the clamping force becomes smaller than about 300 pN, the number of intermediate configurations increases dramatically, where almost all unfolding events at 100 pN involve an intermediate configuration. By directly calculating the life times of the intermediate configurations from the height of the barriers that were crossed on the potential energy surface, we demonstrate that these intermediate states were likely not observed experimentally due to their lifetimes typically being about two orders of magnitude smaller than the experimental temporal resolution.
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Affiliation(s)
- Penghui Cao
- Department of Mechanical Engineering, Boston University, Boston, MA 02215
| | - Gwonchan Yoon
- 1] Department of Mechanical Engineering, Boston University, Boston, MA 02215 [2] Department of Mechanical Engineering, Korea University, Seoul 136-701, South Korea
| | - Weiwei Tao
- Department of Mechanical Engineering, Boston University, Boston, MA 02215
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Harold S Park
- Department of Mechanical Engineering, Boston University, Boston, MA 02215
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50
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Krupička M, Marx D. Disfavoring Mechanochemical Reactions by Stress-Induced Steric Hindrance. J Chem Theory Comput 2015; 11:841-6. [DOI: 10.1021/ct501058a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Martin Krupička
- Lehrstuhl
für Theoretische
Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl
für Theoretische
Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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