1
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Wang H, He K, Zhang H, Zhang Q, Cao L, Li J, Zhong Z, Chen H, Zhou L, Lian C, Wang M, Chen K, Qian PY, Li C. Deciphering deep-sea chemosynthetic symbiosis by single-nucleus RNA-sequencing. eLife 2024; 12:RP88294. [PMID: 39102287 PMCID: PMC11299980 DOI: 10.7554/elife.88294] [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] [Indexed: 08/06/2024] Open
Abstract
Bathymodioline mussels dominate deep-sea methane seep and hydrothermal vent habitats and obtain nutrients and energy primarily through chemosynthetic endosymbiotic bacteria in the bacteriocytes of their gill. However, the molecular mechanisms that orchestrate mussel host-symbiont interactions remain unclear. Here, we constructed a comprehensive cell atlas of the gill in the mussel Gigantidas platifrons from the South China Sea methane seeps (1100 m depth) using single-nucleus RNA-sequencing (snRNA-seq) and whole-mount in situ hybridisation. We identified 13 types of cells, including three previously unknown ones, and uncovered unknown tissue heterogeneity. Every cell type has a designated function in supporting the gill's structure and function, creating an optimal environment for chemosynthesis, and effectively acquiring nutrients from the endosymbiotic bacteria. Analysis of snRNA-seq of in situ transplanted mussels clearly showed the shifts in cell state in response to environmental oscillations. Our findings provide insight into the principles of host-symbiont interaction and the bivalves' environmental adaption mechanisms.
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Affiliation(s)
- Hao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Laoshan LaboratoryQingdaoChina
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Department of Ocean Science, Hong Kong University of Science and TechnologyHong KongChina
| | - Kai He
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou UniversityGuangzhouChina
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingJapan
| | - Lei Cao
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Jing Li
- South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Hao Chen
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Li Zhou
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Chao Lian
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Minxiao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and TechnologyKunmingJapan
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)GuangzhouChina
- Department of Ocean Science, Hong Kong University of Science and TechnologyHong KongChina
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
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2
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Linke WA. Stretching the story of titin and muscle function. J Biomech 2023; 152:111553. [PMID: 36989971 DOI: 10.1016/j.jbiomech.2023.111553] [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: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
The discovery of the giant protein titin, also known as connectin, dates almost half a century back. In this review, I recapitulate major advances in the discovery of the titin filaments and the recognition of their properties and function until today. I briefly discuss how our understanding of the layout and interactions of titin in muscle sarcomeres has evolved and review key facts about the titin sequence at the gene (TTN) and protein levels. I also touch upon properties of titin important for the stability of the contractile units and the assembly and maintenance of sarcomeric proteins. The greater part of my discussion centers around the mechanical function of titin in skeletal muscle. I cover milestones of research on titin's role in stretch-dependent passive tension development, recollect the reasons behind the enormous elastic diversity of titin, and provide an update on the molecular mechanisms of titin elasticity, details of which are emerging even now. I reflect on current knowledge of how muscle fibers behave mechanically if titin stiffness is removed and how titin stiffness can be dynamically regulated, such as by posttranslational modifications or calcium binding. Finally, I highlight novel and exciting, but still controversially discussed, insight into the role titin plays in active tension development, such as length-dependent activation and contraction from longer muscle lengths.
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Affiliation(s)
- Wolfgang A Linke
- Institute of Physiology II, University of Münster, Germany; Clinic for Cardiology and Pneumology, University Medical Center Göttingen, Germany; German Centre for Cardiovascular Research, Berlin, Germany.
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3
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Alraawi Z, Banerjee N, Mohanty S, Kumar TKS. Amyloidogenesis: What Do We Know So Far? Int J Mol Sci 2022; 23:ijms232213970. [PMID: 36430450 PMCID: PMC9695042 DOI: 10.3390/ijms232213970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.
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Affiliation(s)
- Zeina Alraawi
- Department of Chemistry and Biochemistry, Fulbright College of Art and Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Nayan Banerjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Srujana Mohanty
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India
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4
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Galvanetto N, Ye Z, Marchesi A, Mortal S, Maity S, Laio A, Torre VA. Unfolding and identification of membrane proteins in situ. eLife 2022; 11:77427. [PMID: 36094473 PMCID: PMC9531951 DOI: 10.7554/elife.77427] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Single-molecule force spectroscopy (SMFS) uses the cantilever tip of an AFM to apply a force able to unfold a single protein. The obtained force-distance curve encodes the unfolding pathway, and from its analysis it is possible to characterize the folded domains. SMFS has been mostly used to study the unfolding of purified proteins, in solution or reconstituted in a lipid bilayer. Here, we describe a pipeline for analyzing membrane proteins based on SMFS, that involves the isolation of the plasma membrane of single cells and the harvesting of force-distance curves directly from it. We characterized and identified the embedded membrane proteins combining, within a Bayesian framework, the information of the shape of the obtained curves, with the information from Mass Spectrometry and proteomic databases. The pipeline was tested with purified/reconstituted proteins and applied to five cell types where we classified the unfolding of their most abundant membrane proteins. We validated our pipeline by overexpressing 4 constructs, and this allowed us to gather structural insights of the identified proteins, revealing variable elements in the loop regions. Our results set the basis for the investigation of the unfolding of membrane proteins in situ, and for performing proteomics from a membrane fragment.
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Affiliation(s)
| | - Zhongjie Ye
- International School for Advanced Studies, Trieste, Italy
| | - Arin Marchesi
- Nano Life Science Institute, Kanazawa Medical University, Kanazawa, Japan
| | - Simone Mortal
- International School for Advanced Studies, Trieste, Italy
| | - Sourav Maity
- Moleculaire Biofysica, University of Groningen, Groningen, Netherlands
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5
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Gil-Redondo JC, Weber A, Toca-Herrera JL. Measuring (biological) materials mechanics with atomic force microscopy. 3. Mechanical unfolding of biopolymers. Microsc Res Tech 2022; 85:3025-3036. [PMID: 35502131 PMCID: PMC9543778 DOI: 10.1002/jemt.24136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Biopolymers, such as polynucleotides, polypeptides and polysaccharides, are macromolecules that direct most of the functions in living beings. Studying the mechanical unfolding of biopolymers provides important information about their molecular elasticity and mechanical stability, as well as their energy landscape, which is especially important in proteins, since their three‐dimensional structure is essential for their correct activity. In this primer, we present how to study the mechanical properties of proteins with atomic force microscopy and how to obtain information about their stability and energetic landscape. In particular, we discuss the preparation of polyprotein constructs suitable for AFM single molecule force spectroscopy (SMFS), describe the parameters used in our force‐extension SMFS experiments and the models and equations employed in the analysis of the data. As a practical example, we show the effect of the temperature on the unfolding force, the distance to the transition state, the unfolding rate at zero force, the height of the transition state barrier, and the spring constant of the protein for a construct containing nine repeats of the I27 domain from the muscle protein titin.
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Affiliation(s)
- Juan Carlos Gil-Redondo
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Andreas Weber
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - José L Toca-Herrera
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
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6
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Lipke PN, Rauceo JM, Viljoen A. Cell-Cell Mating Interactions: Overview and Potential of Single-Cell Force Spectroscopy. Int J Mol Sci 2022; 23:ijms23031110. [PMID: 35163034 PMCID: PMC8835621 DOI: 10.3390/ijms23031110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
It is an understatement that mating and DNA transfer are key events for living organisms. Among the traits needed to facilitate mating, cell adhesion between gametes is a universal requirement. Thus, there should be specific properties for the adhesion proteins involved in mating. Biochemical and biophysical studies have revealed structural information about mating adhesins, as well as their specificities and affinities, leading to some ideas about these specialized adhesion proteins. Recently, single-cell force spectroscopy (SCFS) has added important findings. In SCFS, mating cells are brought into contact in an atomic force microscope (AFM), and the adhesive forces are monitored through the course of mating. The results have shown some remarkable characteristics of mating adhesins and add knowledge about the design and evolution of mating adhesins.
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Affiliation(s)
- Peter N. Lipke
- Biology Department, Brooklyn College of the City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Correspondence: (P.N.L.); (A.V.)
| | - Jason M. Rauceo
- Department of Sciences, John Jay College of the City University of New York, New York, NY 10019, USA;
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4–5, bte L7.07.07, 1348 Louvain-la-Neuve, Belgium
- Correspondence: (P.N.L.); (A.V.)
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7
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Morris CJ, Zawieja DC, Moore JE. A multiscale sliding filament model of lymphatic muscle pumping. Biomech Model Mechanobiol 2021; 20:2179-2202. [PMID: 34476656 PMCID: PMC8595193 DOI: 10.1007/s10237-021-01501-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 08/01/2021] [Indexed: 11/30/2022]
Abstract
The lymphatics maintain fluid balance by returning interstitial fluid to veins via contraction/compression of vessel segments with check valves. Disruption of lymphatic pumping can result in a condition called lymphedema with interstitial fluid accumulation. Lymphedema treatments are often ineffective, which is partially attributable to insufficient understanding of specialized lymphatic muscle lining the vessels. This muscle exhibits cardiac-like phasic contractions and smooth muscle-like tonic contractions to generate and regulate flow. To understand the relationship between this sub-cellular contractile machinery and organ-level pumping, we have developed a multiscale computational model of phasic and tonic contractions in lymphatic muscle and coupled it to a lymphangion pumping model. Our model uses the sliding filament model (Huxley in Prog Biophys Biophys Chem 7:255-318, 1957) and its adaptation for smooth muscle (Mijailovich in Biophys J 79(5):2667-2681, 2000). Multiple structural arrangements of contractile components and viscoelastic elements were trialed but only one provided physiologic results. We then coupled this model with our previous lumped parameter model of the lymphangion to relate results to experiments. We show that the model produces similar pressure, diameter, and flow tracings to experiments on rat mesenteric lymphatics. This model provides the first estimates of lymphatic muscle contraction energetics and the ability to assess the potential effects of sub-cellular level phenomena such as calcium oscillations on lymphangion outflow. The maximum efficiency value predicted (40%) is at the upper end of estimates for other muscle types. Spontaneous calcium oscillations during diastole were found to increase outflow up to approximately 50% in the range of frequencies and amplitudes tested.
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Affiliation(s)
- Christopher J Morris
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - David C Zawieja
- College of Medicine Faculty, Texas A&M University, Texas, USA
| | - James E Moore
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
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8
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Zuo J, Zhan D, Xia J, Li H. Single-Molecule Force Spectroscopy Studies of Missense Titin Mutations That Are Likely Causing Cardiomyopathy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:12128-12137. [PMID: 34618459 PMCID: PMC9150697 DOI: 10.1021/acs.langmuir.1c02006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/20/2021] [Indexed: 06/13/2023]
Abstract
The giant muscle protein titin plays important roles in heart function. Mutations in titin have emerged as a major cause of familial cardiomyopathy. Missense mutations have been identified in cardiomyopathy patients; however, it is challenging to distinguish disease-causing mutations from benign ones. Given the importance of titin mechanics in heart function, it is critically important to elucidate the mechano-phenotypes of cardiomyopathy-causing mutations found in the elastic I-band part of cardiac titin. Using single-molecule atomic force microscopy (AFM) and equilibrium chemical denaturation, we investigated the mechanical and thermodynamic effects of two missense mutations, R57C-I94 and S22P-I84, found in the elastic I-band part of cardiac titin that were predicted to be likely causing cardiomyopathy by bioinformatics analysis. Our AFM results showed that mutation R57C had a significant destabilization effect on the I94 module. R57C reduced the mechanical unfolding force of I94 by ∼30-40 pN, accelerated the unfolding kinetics, and decelerated the folding. These effects collectively increased the unfolding propensity of I94, likely resulting in altered titin elasticity. In comparison, S22P led to only modest destabilization of I84, with a decrease in unfolding force by ∼10 pN. It is unlikely that such a modest destabilization would lead to a change in titin elasticity. These results will serve as the first step toward elucidating mechano-phenotypes of cardiomyopathy-causing mutations in the elastic I-band.
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9
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Mapplebeck S, Booth J, Shalashilin D. Simulation of protein pulling dynamics on second time scale with boxed molecular dynamics. J Chem Phys 2021; 155:085101. [PMID: 34470356 DOI: 10.1063/5.0059321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We demonstrate how recently developed Boxed Molecular Dynamics (BXD) and kinetics [D. V. Shalashilin et al., J. Chem. Phys. 137, 165102 (2012)] can provide a kinetic description of protein pulling experiments, allowing for a connection to be made between experiment and the atomistic protein structure. BXD theory applied to atomic force microscopy unfolding is similar in spirit to the kinetic two-state model [A. Noy and R. W. Friddle, Methods 60, 142 (2013)] but with some differences. First, BXD uses a large number of boxes, and therefore, it is not a two-state model. Second, BXD rate coefficients are obtained from atomistic molecular dynamics simulations. BXD can describe the dependence of the pulling force on pulling speed. Similar to Shalashilin et al. [J. Chem. Phys. 137, 165102 (2012)], we show that BXD is able to model the experiment at a very long time scale up to seconds, which is way out of reach for standard molecular dynamics.
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Affiliation(s)
- Sarah Mapplebeck
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Jonathan Booth
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
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10
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Li Q, Apostolidou D, Marszalek PE. Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations. Methods 2021; 197:39-53. [PMID: 34020035 DOI: 10.1016/j.ymeth.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/29/2022] Open
Abstract
Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive structure. However, the assignment of force peaks to specific repeats undergoing mechanical unraveling is complicated because all repeats are similar and they interact with their neighbors and form a contiguous tertiary structure. Here, we describe in detail a combination of experimental and computational single-molecule force spectroscopy methods that proved useful for examining the mechanical unfolding and refolding pathways of ankyrin repeat proteins. Specifically, we explain and delineate the use of atomic force microscope-based single molecule force spectroscopy (SMFS) to record the mechanical unfolding behavior of ankyrin repeat proteins and capture their unusually strong refolding propensity that is responsible for generating impressive refolding force peaks. We also describe Coarse Grain Steered Molecular Dynamic (CG-SMD) simulations which complement the experimental observations and provide insights in understanding the unfolding and refolding of these proteins. In addition, we advocate the use of novel coiled-coils-based mechanical polypeptide probes which we developed to demonstrate the vectorial character of folding and refolding of these repeat proteins. The combination of AFM-based SMFS on native and CC-equipped proteins with CG-SMD simulations is powerful not only for ankyrin repeat polypeptides, but also for other repeat proteins and more generally to various multidomain, non-repetitive proteins with complex topologies.
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Affiliation(s)
- Qing Li
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States.
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11
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Bowser BH, Wang S, Kouznetsova TB, Beech HK, Olsen BD, Rubinstein M, Craig SL. Single-Event Spectroscopy and Unravelling Kinetics of Covalent Domains Based on Cyclobutane Mechanophores. J Am Chem Soc 2021; 143:5269-5276. [PMID: 33783187 DOI: 10.1021/jacs.1c02149] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mechanochemical reactions that lead to an increase in polymer contour length have the potential to serve as covalent synthetic mimics of the mechanical unfolding of noncovalent "stored length" domains in structural proteins. Here we report the force-dependent kinetics of stored length release in a family of covalent domain polymers based on cis-1,2-substituted cyclobutane mechanophores. The stored length is determined by the size (n) of a fused ring in an [n.2.0] bicyclic architecture, and it can be made sufficiently large (>3 nm per event) that individual unravelling events are resolved in both constant-velocity and constant-force single-molecule force spectroscopy (SMFS) experiments. Replacing a methylene in the pulling attachment with a phenyl group drops the force necessary to achieve rate constants of 1 s-1 from ca. 1970 pN (dialkyl handles) to 630 pN (diaryl handles), and the substituent effect is attributed to a combination of electronic stabilization and mechanical leverage effects. In contrast, the kinetics are negligibly perturbed by changes in the amount of stored length. The independent control of unravelling force and extension holds promise as a probe of molecular behavior in polymer networks and for optimizing the behaviors of materials made from covalent domain polymers.
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Affiliation(s)
- Brandon H Bowser
- NSF Center for the Chemistry of Molecularly Optimized Networks, Duke University, Durham, North Carolina 27708, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Shu Wang
- NSF Center for the Chemistry of Molecularly Optimized Networks, Duke University, Durham, North Carolina 27708, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Tatiana B Kouznetsova
- NSF Center for the Chemistry of Molecularly Optimized Networks, Duke University, Durham, North Carolina 27708, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Haley K Beech
- NSF Center for the Chemistry of Molecularly Optimized Networks, Duke University, Durham, North Carolina 27708, United States.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley D Olsen
- NSF Center for the Chemistry of Molecularly Optimized Networks, Duke University, Durham, North Carolina 27708, United States.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael Rubinstein
- NSF Center for the Chemistry of Molecularly Optimized Networks, Duke University, Durham, North Carolina 27708, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Departments of Physics, Mechanical Engineering and Materials Science, and Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States.,World Premier Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, Japan
| | - Stephen L Craig
- NSF Center for the Chemistry of Molecularly Optimized Networks, Duke University, Durham, North Carolina 27708, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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12
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Shoham A, Givli S. Unfolding compactly folded molecular domains: Overall stiffness modifies the force-barrier relation. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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13
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Chen MP, Kiduko SA, Saad NS, Canan BD, Kilic A, Mohler PJ, Janssen PML. Stretching single titin molecules from failing human hearts reveals titin's role in blunting cardiac kinetic reserve. Cardiovasc Res 2020; 116:127-137. [PMID: 30778519 DOI: 10.1093/cvr/cvz043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/08/2018] [Accepted: 02/13/2019] [Indexed: 11/15/2022] Open
Abstract
AIMS Heart failure (HF) patients commonly experience symptoms primarily during elevated heart rates, as a result of physical activities or stress. A main determinant of diastolic passive tension, the elastic sarcomeric protein titin, has been shown to be associated with HF, with unresolved involvement regarding its role at different heart rates. To determine whether titin is playing a role in the heart rate (frequency-) dependent acceleration of relaxation (FDAR). W, we studied the FDAR responses in live human left ventricular cardiomyocytes and the corresponding titin-based passive tension (TPT) from failing and non-failing human hearts. METHODS AND RESULTS Using atomic force, we developed a novel single-molecule force spectroscopy approach to detect TPT based on the frequency-modulated cardiac cycle. Mean TPT reduced upon an increased heart rate in non-failing human hearts, while this reduction was significantly blunted in failing human hearts. These mechanical changes in the titin distal Ig domain significantly correlated with the frequency-dependent relaxation kinetics of human cardiomyocytes obtained from the corresponding hearts. Furthermore, the data suggested that the higher the TPT, the faster the cardiomyocytes relaxed, but the lower the potential of myocytes to speed up relaxation at a higher heart rate. Such poorer FDAR response was also associated with a lesser reduction or a bigger increase in TPT upon elevated heart rate. CONCLUSIONS Our study established a novel approach in detecting dynamic heart rate relevant tension changes physiologically on native titin domains. Using this approach, the data suggested that the regulation of kinetic reserve in cardiac relaxation and its pathological changes were associated with the intensity and dynamic changes of passive tension by titin.
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Affiliation(s)
- Mei-Pian Chen
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA
| | - Salome A Kiduko
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA
| | - Nancy S Saad
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Benjamin D Canan
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA
| | - Ahmet Kilic
- Division of Cardiothoracic Surgery, Department of Surgery, The Ohio State University Wexner Medical Center, 410 W 10th Ave, Columbus, OH 43210, USA
| | - Peter J Mohler
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA.,Department of Internal Medicine, The Ohio State University Wexner Medical Center, 395 W 12th Ave, Columbus, OH 43210, USA
| | - Paul M L Janssen
- Department of Physiology and Cell Biology, The Ohio State University, Hamilton Hall 207a, 1645 Neil Avenue, Columbus, OH 43210, USA.,Dorothy M. Davis Heart and Lung Research Institute, 473 W 12th Ave, Columbus, OH 43210 USA.,Department of Internal Medicine, The Ohio State University Wexner Medical Center, 395 W 12th Ave, Columbus, OH 43210, USA
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14
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Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
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Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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15
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Werten MWT, Eggink G, Cohen Stuart MA, de Wolf FA. Production of protein-based polymers in Pichia pastoris. Biotechnol Adv 2019; 37:642-666. [PMID: 30902728 PMCID: PMC6624476 DOI: 10.1016/j.biotechadv.2019.03.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 02/03/2019] [Accepted: 03/17/2019] [Indexed: 01/09/2023]
Abstract
Materials science and genetic engineering have joined forces over the last three decades in the development of so-called protein-based polymers. These are proteins, typically with repetitive amino acid sequences, that have such physical properties that they can be used as functional materials. Well-known natural examples are collagen, silk, and elastin, but also artificial sequences have been devised. These proteins can be produced in a suitable host via recombinant DNA technology, and it is this inherent control over monomer sequence and molecular size that renders this class of polymers of particular interest to the fields of nanomaterials and biomedical research. Traditionally, Escherichia coli has been the main workhorse for the production of these polymers, but the methylotrophic yeast Pichia pastoris is finding increased use in view of the often high yields and potential bioprocessing benefits. We here provide an overview of protein-based polymers produced in P. pastoris. We summarize their physicochemical properties, briefly note possible applications, and detail their biosynthesis. Some challenges that may be faced when using P. pastoris for polymer production are identified: (i) low yields and poor process control in shake flask cultures; i.e., the need for bioreactors, (ii) proteolytic degradation, and (iii) self-assembly in vivo. Strategies to overcome these challenges are discussed, which we anticipate will be of interest also to readers involved in protein expression in P. pastoris in general.
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Affiliation(s)
- Marc W T Werten
- Wageningen Food & Biobased Research, NL-6708 WG Wageningen, The Netherlands.
| | - Gerrit Eggink
- Wageningen Food & Biobased Research, NL-6708 WG Wageningen, The Netherlands; Bioprocess Engineering, Wageningen University & Research, NL-6708 PB Wageningen, The Netherlands
| | - Martien A Cohen Stuart
- Physical Chemistry and Soft Matter, Wageningen University & Research, NL-6708 WE Wageningen, The Netherlands
| | - Frits A de Wolf
- Wageningen Food & Biobased Research, NL-6708 WG Wageningen, The Netherlands
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16
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Mártonfalvi Z, Bianco P, Naftz K, Ferenczy GG, Kellermayer M. Force generation by titin folding. Protein Sci 2017; 26:1380-1390. [PMID: 28097712 DOI: 10.1002/pro.3117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/08/2017] [Accepted: 01/09/2017] [Indexed: 12/19/2022]
Abstract
Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (<10 pN), extension fluctuated without resolvable discrete events. In position-clamp experiments, the time-dependent force trace contained rapid fluctuations and a gradual increase of average force, indicating that titin can develop force via dynamic transitions between its structural states en route to the native conformation. In 4 M urea, which destabilizes H-bonds hence the consolidated native domain structure, the net force increase disappeared but the fluctuations persisted. Thus, whereas net force generation is caused by the ensemble folding of the elastically-coupled domains, force fluctuations arise due to a dynamic equilibrium between unfolded and molten-globule states. Monte-Carlo simulations incorporating a compact molten-globule intermediate in the folding landscape recovered all features of our nanomechanics results. The ensemble molten-globule dynamics delivers significant added contractility that may assist sarcomere mechanics, and it may reduce the dissipative energy loss associated with titin unfolding/refolding during muscle contraction/relaxation cycles.
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Affiliation(s)
- Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest H1094, Hungary
| | - Pasquale Bianco
- Physiolab, Department of Biology, University of Florence, 50019 Sesto Fiorentino, FI, Italy
| | - Katalin Naftz
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest H1094, Hungary
| | - György G Ferenczy
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest H1094, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest H1094, Hungary.,MTA-SE Molecular Biophysics Research Group, Semmelweis University, Budapest H1094, Hungary
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17
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The Power of Force: Insights into the Protein Folding Process Using Single-Molecule Force Spectroscopy. J Mol Biol 2016; 428:4245-4257. [PMID: 27639437 DOI: 10.1016/j.jmb.2016.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 01/03/2023]
Abstract
One of the major challenges in modern biophysics is observing and understanding conformational changes during complex molecular processes, from the fundamental protein folding to the function of molecular machines. Single-molecule techniques have been one of the major driving forces of the huge progress attained in the last few years. Recent advances in resolution of the experimental setups, aided by theoretical developments and molecular dynamics simulations, have revealed a much higher degree of complexity inside these molecular processes than previously reported using traditional ensemble measurements. This review sums up the evolution of these developments and gives an outlook on prospective discoveries.
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18
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Popa I, Rivas-Pardo JA, Eckels EC, Echelman DJ, Badilla CL, Valle-Orero J, Fernández JM. A HaloTag Anchored Ruler for Week-Long Studies of Protein Dynamics. J Am Chem Soc 2016; 138:10546-53. [PMID: 27409974 PMCID: PMC5510598 DOI: 10.1021/jacs.6b05429] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Under physiological conditions, protein oxidation and misfolding occur with very low probability and on long times scales. Single-molecule techniques provide the ability to distinguish between properly folded and damaged proteins that are otherwise masked in ensemble measurements. However, at physiological conditions these rare events occur with a time constant of several hours, inaccessible to current single-molecule approaches. Here we present a magnetic-tweezers-based technique that allows, for the first time, the study of folding of single proteins during week-long experiments. This technique combines HaloTag anchoring, sub-micrometer positioning of magnets, and an active correction of the focal drift. Using this technique and protein L as a molecular template, we generate a magnet law by correlating the distance between the magnet and the measuring paramagnetic bead with unfolding/folding steps. We demonstrate that, using this magnet law, we can accurately measure the dynamics of proteins over a wide range of forces, with minimal dispersion from bead to bead. We also show that the force calibration remains invariant over week-long experiments applied to the same single proteins. The approach demonstrated in this Article opens new, exciting ways to examine proteins on the "human" time scale and establishes magnetic tweezers as a valuable technique to study low-probability events that occur during protein folding under force.
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Affiliation(s)
- Ionel Popa
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Jaime Andrés Rivas-Pardo
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Edward C Eckels
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Daniel J Echelman
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Carmen L Badilla
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Jessica Valle-Orero
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
| | - Julio M Fernández
- Department of Biological Sciences, Columbia University , 1212 Amsterdam Avenue, New York, New York 10027, United States
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19
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Connecting thermal and mechanical protein (un)folding landscapes. Biophys J 2016; 107:2950-2961. [PMID: 25517160 DOI: 10.1016/j.bpj.2014.10.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/08/2014] [Accepted: 10/15/2014] [Indexed: 11/22/2022] Open
Abstract
Molecular dynamics simulations supplement single-molecule pulling experiments by providing the possibility of examining the full free energy landscape using many coordinates. Here, we use an all-atom structure-based model to study the force and temperature dependence of the unfolding of the protein filamin by applying force at both termini. The unfolding time-force relation τ(F) indicates that the force-induced unfolding behavior of filamin can be characterized into three regimes: barrier-limited low- and intermediate-force regimes, and a barrierless high-force regime. Slope changes of τ(F) separate the three regimes. We show that the behavior of τ(F) can be understood from a two-dimensional free energy landscape projected onto the extension X and the fraction of native contacts Q. In the low-force regime, the unfolding rate is roughly force-independent due to the small (even negative) separation in X between the native ensemble and transition state ensemble (TSE). In the intermediate-force regime, force sufficiently separates the TSE from the native ensemble such that τ(F) roughly follows an exponential relation. This regime is typically explored by pulling experiments. While X may fail to resolve the TSE due to overlap with the unfolded ensemble just below the folding temperature, the overlap is minimal at lower temperatures where experiments are likely to be conducted. The TSE becomes increasingly structured with force, whereas the average order of structural events during unfolding remains roughly unchanged. The high-force regime is characterized by barrierless unfolding, and the unfolding time approaches a limit of ∼10 μs for the highest forces we studied. Finally, a combination of X and Q is shown to be a good reaction coordinate for almost the entire force range.
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20
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Oroz J, Bruix M, Laurents D, Galera-Prat A, Schönfelder J, Cañada F, Carrión-Vázquez M. The Y9P Variant of the Titin I27 Module: Structural Determinants of Its Revisited Nanomechanics. Structure 2016; 24:606-616. [DOI: 10.1016/j.str.2016.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/30/2015] [Accepted: 02/22/2016] [Indexed: 11/28/2022]
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21
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Abstract
Vascular smooth muscle (VSM; see Table 1 for a list of abbreviations) is a heterogeneous biomaterial comprised of cells and extracellular matrix. By surrounding tubes of endothelial cells, VSM forms a regulated network, the vasculature, through which oxygenated blood supplies specialized organs, permitting the development of large multicellular organisms. VSM cells, the engine of the vasculature, house a set of regulated nanomotors that permit rapid stress-development, sustained stress-maintenance and vessel constriction. Viscoelastic materials within, surrounding and attached to VSM cells, comprised largely of polymeric proteins with complex mechanical characteristics, assist the engine with countering loads imposed by the heart pump, and with control of relengthening after constriction. The complexity of this smart material can be reduced by classical mechanical studies combined with circuit modeling using spring and dashpot elements. Evaluation of the mechanical characteristics of VSM requires a more complete understanding of the mechanics and regulation of its biochemical parts, and ultimately, an understanding of how these parts work together to form the machinery of the vascular tree. Current molecular studies provide detailed mechanical data about single polymeric molecules, revealing viscoelasticity and plasticity at the protein domain level, the unique biological slip-catch bond, and a regulated two-step actomyosin power stroke. At the tissue level, new insight into acutely dynamic stress-strain behavior reveals smooth muscle to exhibit adaptive plasticity. At its core, physiology aims to describe the complex interactions of molecular systems, clarifying structure-function relationships and regulation of biological machines. The intent of this review is to provide a comprehensive presentation of one biomachine, VSM.
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Affiliation(s)
- Paul H Ratz
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
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22
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Pletikapić G, Lannon H, Murvai Ü, Kellermayer MSZ, Svetličić V, Brujic J. Self-assembly of polysaccharides gives rise to distinct mechanical signatures in marine gels. Biophys J 2015; 107:355-364. [PMID: 25028877 DOI: 10.1016/j.bpj.2014.04.065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/10/2014] [Accepted: 04/28/2014] [Indexed: 12/13/2022] Open
Abstract
Marine-gel biopolymers were recently visualized at the molecular level using atomic force microscopy (AFM) to reveal fine fibril-forming networks with low to high degrees of cross-linking. In this work, we use force spectroscopy to quantify the intra- and intermolecular forces within the marine-gel network. Combining force measurements, AFM imaging, and the known chemical composition of marine gels allows us to identify the microscopic origins of distinct mechanical responses. At the single-fibril level, we uncover force-extension curves that resemble those of individual polysaccharide fibrils. They exhibit entropic elasticity followed by extensions associated with chair-to-boat transitions specific to the type of polysaccharide at high forces. Surprisingly, a low degree of cross-linking leads to sawtooth patterns that we attribute to the unraveling of polysaccharide entanglements. At a high degree of cross-linking, we observe force plateaus that arise from unzipping, as well as unwinding, of helical bundles. Finally, the complex 3D network structure gives rise to force staircases of increasing height that correspond to the hierarchical peeling of fibrils away from the junction zones. In addition, we show that these diverse mechanical responses also arise in reconstituted polysaccharide gels, which highlights their dominant role in the mechanical architecture of marine gels.
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Affiliation(s)
- G Pletikapić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - H Lannon
- Center for Soft Matter Research and Department of Physics, New York University, New York, New York
| | - Ü Murvai
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - M S Z Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - V Svetličić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - J Brujic
- Center for Soft Matter Research and Department of Physics, New York University, New York, New York.
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23
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Lun AS, Chen J, Lange S. Probing muscle ankyrin-repeat protein (MARP) structure and function. Anat Rec (Hoboken) 2015; 297:1615-29. [PMID: 25125175 DOI: 10.1002/ar.22968] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/02/2014] [Indexed: 12/20/2022]
Abstract
Muscle ankyrin-repeat proteins (MARPs) have been shown to serve diverse functions within cardiac and skeletal muscle cells. Apart from their interactions with sarcomeric proteins like titin or myopalladin that locate them along myofilaments, MARPs are able to shuttle to the nucleus where they act as modulators for a variety of transcription factors. The deregulation of MARPs in many cardiac and skeletal myopathies contributes to their use as biomarkers for these diseases. Many of their functions are attributed to their domain composition. MARPs consist of an N-terminal coiled-coil domain responsible for their dimerization. The C-terminus contains a series of ankyrin repeats, whose best-characterized function is to bind to the N2A region of the giant sarcomeric protein titin. Here we investigate the nature of their dimerization and their interaction with titin more closely. We demonstrate that the coiled-coil domain in all MARPs enables their homo- and hetero-dimerization in antiparallel fashion. Protein complementation experiments indicate further antiparallel binding of the ankyrin repeats to titin's N2A region. Binding of MARP to titin also affects its PKA mediated phosphorylation. We demonstrate further that MARPs themselves are phosphorylated by PKA and PKC, potentially altering their structure or function. These studies elucidate structural relationships within the stretch-responsive MARP/titin complex in cross-striated muscle cells, and may relate to disease relevant posttranslational modifications of MARPs and titin that alter muscle compliance.
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24
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Abstract
The giant protein titin forms a unique filament network in cardiomyocytes, which engages in both mechanical and signaling functions of the heart. TTN, which encodes titin, is also a major human disease gene. In this review, we cover the roles of cardiac titin in normal and failing hearts, with a special emphasis on the contribution of titin to diastolic stiffness. We provide an update on disease-associated titin mutations in cardiac and skeletal muscles and summarize what is known about the impact of protein-protein interactions on titin properties and functions. We discuss the importance of titin-isoform shifts and titin phosphorylation, as well as titin modifications related to oxidative stress, in adjusting the diastolic stiffness of the healthy and the failing heart. Along the way we distinguish among titin alterations in systolic and in diastolic heart failure and ponder the evidence for titin stiffness as a potential target for pharmacological intervention in heart disease.
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Affiliation(s)
- Wolfgang A Linke
- From the Department of Cardiovascular Physiology, Ruhr University Bochum, Bochum, Germany
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25
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Buyandelger B, Mansfield C, Knöll R. Mechano-signaling in heart failure. Pflugers Arch 2014; 466:1093-9. [PMID: 24531746 PMCID: PMC4033803 DOI: 10.1007/s00424-014-1468-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 02/07/2023]
Abstract
Mechanosensation and mechanotransduction are fundamental aspects of biology, but the link between physical stimuli and biological responses remains not well understood. The perception of mechanical stimuli, their conversion into biochemical signals, and the transmission of these signals are particularly important for dynamic organs such as the heart. Various concepts have been introduced to explain mechanosensation at the molecular level, including effects on signalosomes, tensegrity, or direct activation (or inactivation) of enzymes. Striated muscles, including cardiac myocytes, differ from other cells in that they contain sarcomeres which are essential for the generation of forces and which play additional roles in mechanosensation. The majority of cardiomyopathy causing candidate genes encode structural proteins among which titin probably is the most important one. Due to its elastic elements, titin is a length sensor and also plays a role as a tension sensor (i.e., stress sensation). The recent discovery of titin mutations being a major cause of dilated cardiomyopathy (DCM) also underpins the importance of mechanosensation and mechanotransduction in the pathogenesis of heart failure. Here, we focus on sarcomere-related mechanisms, discuss recent findings, and provide a link to cardiomyopathy and associated heart failure.
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Affiliation(s)
- Byambajav Buyandelger
- Imperial College, British Heart Foundation-Centre for Research Excellence, National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
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26
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Kötter S, Unger A, Hamdani N, Lang P, Vorgerd M, Nagel-Steger L, Linke WA. Human myocytes are protected from titin aggregation-induced stiffening by small heat shock proteins. ACTA ACUST UNITED AC 2014; 204:187-202. [PMID: 24421331 PMCID: PMC3897184 DOI: 10.1083/jcb.201306077] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Small heat shock proteins translocate to unfolded titin Ig domains under stress conditions to prevent titin aggregation and myocyte stiffening. In myocytes, small heat shock proteins (sHSPs) are preferentially translocated under stress to the sarcomeres. The functional implications of this translocation are poorly understood. We show here that HSP27 and αB-crystallin associated with immunoglobulin-like (Ig) domain-containing regions, but not the disordered PEVK domain (titin region rich in proline, glutamate, valine, and lysine), of the titin springs. In sarcomeres, sHSP binding to titin was actin filament independent and promoted by factors that increased titin Ig unfolding, including sarcomere stretch and the expression of stiff titin isoforms. Titin spring elements behaved predominantly as monomers in vitro. However, unfolded Ig segments aggregated, preferentially under acidic conditions, and αB-crystallin prevented this aggregation. Disordered regions did not aggregate. Promoting titin Ig unfolding in cardiomyocytes caused elevated stiffness under acidic stress, but HSP27 or αB-crystallin suppressed this stiffening. In diseased human muscle and heart, both sHSPs associated with the titin springs, in contrast to the cytosolic/Z-disk localization seen in healthy muscle/heart. We conclude that aggregation of unfolded titin Ig domains stiffens myocytes and that sHSPs translocate to these domains to prevent this aggregation.
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Affiliation(s)
- Sebastian Kötter
- Department of Cardiovascular Physiology and 2 Neurological University Clinic Bergmannsheil, Ruhr University Bochum, 44780 Bochum, Germany
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27
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Scholl ZN, Li Q, Marszalek PE. Single molecule mechanical manipulation for studying biological properties of proteins,
DNA
, and sugars. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 6:211-29. [DOI: 10.1002/wnan.1253] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/10/2013] [Accepted: 10/17/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Zackary N. Scholl
- Department of Computational Biology and Bioinformatics Duke University Durham NC USA
| | - Qing Li
- Department of Mechanical Engineering and Materials Science Duke University Durham NC USA
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems Duke University Durham NC USA
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28
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Michalek AJ, Howarth JW, Gulick J, Previs MJ, Robbins J, Rosevear PR, Warshaw DM. Phosphorylation modulates the mechanical stability of the cardiac myosin-binding protein C motif. Biophys J 2013; 104:442-52. [PMID: 23442866 DOI: 10.1016/j.bpj.2012.12.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/12/2012] [Accepted: 12/14/2012] [Indexed: 01/21/2023] Open
Abstract
Cardiac myosin-binding protein C (cMyBP-C) is a thick-filament-associated protein that modulates cardiac contractility through interactions of its N-terminal immunoglobulin (Ig)-like C0-C2 domains with actin and/or myosin. These interactions are modified by the phosphorylation of at least four serines located within the motif linker between domains C1 and C2. We investigated whether motif phosphorylation alters its mechanical properties by characterizing force-extension relations using atomic force spectroscopy of expressed mouse N-terminal cMyBP-C fragments (i.e., C0-C3). Protein kinase A phosphorylation or serine replacement with aspartic acids did not affect persistence length (0.43 ± 0.04 nm), individual Ig-like domain unfolding forces (118 ± 3 pN), or Ig extension due to unfolding (30 ± 0.38 nm). However, phosphorylation did significantly decrease the C0-C3 mean contour length by 24 ± 2 nm. These results suggest that upon phosphorylation, the motif, which is freely extensible in the nonphosphorylated state, adopts a more stable and/or different structure. Circular dichroism and dynamic light scattering data for shorter expressed C1-C2 fragments with all four serines replaced by aspartic acids confirmed that the motif did adopt a more stable structure that was not apparent in the nonphosphorylated motif. These biophysical data provide both a mechanical and structural basis for cMyBP-C regulation by motif phosphorylation.
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Affiliation(s)
- Arthur J Michalek
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont, USA
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29
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Carvalho FA, Martins IC, Santos NC. Atomic force microscopy and force spectroscopy on the assessment of protein folding and functionality. Arch Biochem Biophys 2013; 531:116-27. [DOI: 10.1016/j.abb.2012.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/12/2012] [Accepted: 11/20/2012] [Indexed: 12/01/2022]
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30
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Brantley JN, Bailey CB, Wiggins KM, Keatinge-Clay AT, Bielawski CW. Mechanobiochemistry: harnessing biomacromolecules for force-responsive materials. Polym Chem 2013. [DOI: 10.1039/c3py00001j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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31
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DuVall MM, Gifford JL, Amrein M, Herzog W. Altered mechanical properties of titin immunoglobulin domain 27 in the presence of calcium. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 42:301-7. [DOI: 10.1007/s00249-012-0875-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 11/13/2012] [Accepted: 11/16/2012] [Indexed: 12/18/2022]
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32
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Faccioli P, Pederiva F. Microscopically computing free-energy profiles and transition path time of rare macromolecular transitions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:061916. [PMID: 23367984 DOI: 10.1103/physreve.86.061916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 06/01/2023]
Abstract
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In order to sample the ensemble of statistically significant reaction pathways, we define a biased molecular dynamics (MD) in which barrier-crossing transitions are accelerated without introducing any unphysical external force. In contrast to other biased MD methods, in the present approach the systematic errors which are generated in order to accelerate the transition can be analytically calculated and therefore can be corrected for. This allows for a computationally efficient reconstruction of the free-energy profile as a function of the reaction coordinate and for the calculation of the corresponding diffusion coefficient. The transition path time can then be readily evaluated within the dominant reaction pathways approach. We illustrate and test this method by characterizing a thermally activated transition on a two-dimensional energy surface and the folding of a small protein fragment within a coarse-grained model.
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Affiliation(s)
- P Faccioli
- Physics Department, University of Trento, Via Sommarive 14, Povo, I-38129 Trento, Italy
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Titin-based tension in the cardiac sarcomere: molecular origin and physiological adaptations. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 110:204-17. [PMID: 22910434 DOI: 10.1016/j.pbiomolbio.2012.08.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 08/03/2012] [Indexed: 01/08/2023]
Abstract
The passive stiffness of cardiac muscle plays a critical role in ventricular filling during diastole and is determined by the extracellular matrix and the sarcomeric protein titin. Titin spans from the Z-disk to the M-band of the sarcomere and also contains a large extensible region that acts as a molecular spring and develops passive force during sarcomere stretch. This extensible segment is titin's I-band region, and its force-generating mechanical properties determine titin-based passive tension. The properties of titin's I-band region can be modulated by isoform splicing and post-translational modification and are intimately linked to diastolic function. This review discusses the physical origin of titin-based passive tension, the mechanisms that alter titin stiffness, and titin's role in stress-sensing signaling pathways.
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34
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Affiliation(s)
- Elias M. Puchner
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158;
| | - Hermann E. Gaub
- Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany;
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35
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Taniguchi Y, Kobayashi A, Kawakami M. Mechanical unfolding studies of protein molecules. Biophysics (Nagoya-shi) 2012; 8:51-58. [PMID: 27857607 PMCID: PMC5070453 DOI: 10.2142/biophysics.8.51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 12/30/2011] [Indexed: 12/31/2022] Open
Abstract
Atomic force microscopy (AFM) enables the pick up of a single protein molecule to apply a mechanical force. This technique, called "force spectroscopy," provides unique information about the intermediates and free energy landscape of the mechanical unfolding of proteins. In this review, we introduce the AFM-based single molecule force spectroscopy of proteins and describe recent studies that answer some fundamental questions such as "is the mechanical resistance of proteins isotropic?", "what is the structure of the transition state in mechanical unfolding?", and "is mechanical unfolding related to biological functions?"
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Affiliation(s)
- Yukinori Taniguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa Prefecture 923-1292, Japan
| | - Akiko Kobayashi
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa Prefecture 923-1292, Japan
| | - Masaru Kawakami
- School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa Prefecture 923-1292, Japan
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36
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Stahl SW, Puchner EM, Alexandrovich A, Gautel M, Gaub HE. A conditional gating mechanism assures the integrity of the molecular force-sensor titin kinase. Biophys J 2012; 101:1978-86. [PMID: 22004752 DOI: 10.1016/j.bpj.2011.09.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 08/11/2011] [Accepted: 09/06/2011] [Indexed: 12/16/2022] Open
Abstract
As more and more recent investigations point out, force plays an important role in cellular regulation mechanisms. Biological responses to mechanical stress are often based on force-induced conformational changes of single molecules. The force sensor, titin kinase, is involved in a signaling complex that regulates protein turnover and transcriptional adaptation in striated muscle. The structural architecture of such a force sensor determines its response to force and must assure both activity and mechanical integrity, which are prerequisites for its function. Here, we use single-molecule force-clamp spectroscopy to show that titin kinase is organized in such a way that the regulatory domains have to unfold before secondary structure elements that determine the overall fold and catalytic function. The stepwise unfolding over many barriers with a topologically determined sequence assures that the protein can react to force by conformational changes while maintaining its structural integrity.
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Affiliation(s)
- Stefan W Stahl
- Center for NanoScience, Ludwig-Maximilians-University Munich, Munich, Germany
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37
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Ma L, Xu M, Oberhauser AF. Single-molecule force spectroscopy of polycystic kidney disease proteins. Methods Mol Biol 2012; 875:297-310. [PMID: 22573448 DOI: 10.1007/978-1-61779-806-1_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Atomic force microscopy in its single-molecule force spectroscopy mode is a nanomanipulation technique that is extensively used for the study of the mechanical properties of proteins. It is particularly suited to examine their response to stretching (i.e., molecular elasticity and mechanical stability). Here, we describe protein engineering strategies and single-molecule AFM techniques for probing protein mechanics, with special emphasis on polycystic kidney disease (PKD) proteins. We also provide step-by-step protocols for preparing proteins and performing single-molecule force measurements.
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Affiliation(s)
- Liang Ma
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
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38
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Ghosh SK, Ostanin VP, Johnson CL, Lowe CR, Seshia AA. Probing biomolecular interaction forces using an anharmonic acoustic technique for selective detection of bacterial spores. Biosens Bioelectron 2011; 29:145-50. [DOI: 10.1016/j.bios.2011.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 07/08/2011] [Accepted: 08/09/2011] [Indexed: 10/17/2022]
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39
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Zhao X, Wei Y, Wang Z, Zhang B, Chen F, Zhang P. Mechanochemistry in Thermomechanical Processing of Foods: Kinetic Aspects. J Food Sci 2011; 76:R134-42. [DOI: 10.1111/j.1750-3841.2011.02301.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Voelkel T, Linke WA. Conformation-regulated mechanosensory control via titin domains in cardiac muscle. Pflugers Arch 2011; 462:143-54. [PMID: 21347754 PMCID: PMC3114084 DOI: 10.1007/s00424-011-0938-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 12/19/2022]
Abstract
The giant filamentous protein titin is ideally positioned in the muscle sarcomere to sense mechanical stimuli and transform them into biochemical signals, such as those triggering cardiac hypertrophy. In this review, we ponder the evidence for signaling hotspots along the titin filament involved in mechanosensory control mechanisms. On the way, we distinguish between stress and strain as triggers of mechanical signaling events at the cardiac sarcomere. Whereas the Z-disk and M-band regions of titin may be prominently involved in sensing mechanical stress, signaling hotspots within the elastic I-band titin segment may respond primarily to mechanical strain. Common to both stress and strain sensor elements is their regulation by conformational changes in protein domains.
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Affiliation(s)
- Tobias Voelkel
- Department of Cardiovascular Physiology, Institute of Physiology, Ruhr University Bochum, MA 3/56, 44780 Bochum, Germany
| | - Wolfgang A. Linke
- Department of Cardiovascular Physiology, Institute of Physiology, Ruhr University Bochum, MA 3/56, 44780 Bochum, Germany
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41
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Hsin J, Strümpfer J, Lee EH, Schulten K. Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory. Annu Rev Biophys 2011; 40:187-203. [DOI: 10.1146/annurev-biophys-072110-125325] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jen Hsin
- Department of Physics, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801
| | - Johan Strümpfer
- Department of Physics, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, Urbana, Illinois 61801
| | - Eric H. Lee
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, Urbana, Illinois 61801
- College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801;
| | - Klaus Schulten
- Department of Physics, Urbana, Illinois 61801
- Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, Urbana, Illinois 61801
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42
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Three powerful research tools from single cells into single molecules: AFM, laser tweezers, and Raman spectroscopy. Appl Biochem Biotechnol 2011; 165:485-96. [PMID: 21556902 DOI: 10.1007/s12010-011-9267-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 04/18/2011] [Indexed: 01/11/2023]
Abstract
By using three physical techniques (atomic force microscopy (AFM), laser tweezers, and Raman spectroscopy), many excellent works in single-cell/molecule research have been accomplished. In this review, we present a brief introduction to the principles of these three techniques, and their capabilities toward single-cell/molecule research are highlighted. Afterward, the advances in single-cell/molecule research that have been facilitated by these three techniques are described. Following this, their complementary assets for single-cell/molecule research are analyzed, and the necessity of integrating the functions of these three techniques into one instrument is proposed.
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43
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Johansen KM, Forer A, Yao C, Girton J, Johansen J. Do nuclear envelope and intranuclear proteins reorganize during mitosis to form an elastic, hydrogel-like spindle matrix? Chromosome Res 2011; 19:345-65. [DOI: 10.1007/s10577-011-9187-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Krüger M, Linke WA. The giant protein titin: a regulatory node that integrates myocyte signaling pathways. J Biol Chem 2011; 286:9905-12. [PMID: 21257761 DOI: 10.1074/jbc.r110.173260] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Titin, the largest protein in the human body, is well known as a molecular spring in muscle cells and scaffold protein aiding myofibrillar assembly. However, recent evidence has established another important role for titin: that of a regulatory node integrating, and perhaps coordinating, diverse signaling pathways, particularly in cardiomyocytes. We review key findings within this emerging field, including those related to phosphorylation of the titin springs, and also discuss how titin participates in hypertrophic gene regulation and protein quality control.
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Affiliation(s)
- Martina Krüger
- Department of Cardiovascular Physiology, Ruhr University Bochum, D-44780 Bochum, Germany.
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45
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Bornschlögl T, Rief M. Single-molecule protein unfolding and refolding using atomic force microscopy. Methods Mol Biol 2011; 783:233-250. [PMID: 21909892 DOI: 10.1007/978-1-61779-282-3_13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Over the past few years, atomic force microscopy (AFM) became a prominent tool to study the mechanical properties of proteins and protein interactions on a single-molecule level. AFM together with other mechanical, single-molecule manipulating techniques (Bustamante et al., Nat Rev Mol Cell Biol 1:130-136, 2000) made it possible to probe biological molecules in a way that is complementary to single-molecule methods using chemicals or temperature as a denaturant (Borgia et al., Annu Rev Biochem 77:101-125, 2008). For example, AFM offered new insights into the process of protein folding and unfolding by probing single proteins with mechanical forces. Since many proteins fulfill mechanical function or are exerted to mechanical forces in their natural environment, AFM allows to target physiologically relevant questions. Although the number of proteins unfolded with AFM continually increases (Linke and Grutzner, Pflugers Arch 456:101-115, 2008; Zhuang and Rief, Curr Opin Struct Biol 13:88-97, 2003; Clausen-Schaumann et al., Curr Opin Chem Biol 4:524-530, 2000; Rounsevell et al., Methods 34:100-111, 2004), the total number of proteins studied so far is still relatively small (Oberhauser and Carrion-Vazquez, J Biol Chem 283:6617-6621, 2008). This chapter aims at giving protocol-like instructions for people who are actually getting started using AFM to study mechanical protein unfolding or refolding. The instruction includes different approaches to produce polyproteins or modular protein chains which are commonly used to screen for true single-molecule AFM data traces. Also, the basic principles for data collection with AFM and the basic data analysis methods are explained. For people who want to study proteins that unfold at small forces or for people who want to study protein folding which also occurs typically at small forces (<30 pN), an averaging technique is explained, allowing to increase the force resolution in this regime. For topics that would go beyond the scope of this chapter - as, for example, the details about different cantilever calibration methods - references are provided.
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46
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Puolanne E, Halonen M. Theoretical aspects of water-holding in meat. Meat Sci 2010; 86:151-65. [DOI: 10.1016/j.meatsci.2010.04.038] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 04/21/2010] [Accepted: 04/29/2010] [Indexed: 11/15/2022]
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47
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Baclayon M, Roos WH, Wuite GJL. Sampling protein form and function with the atomic force microscope. Mol Cell Proteomics 2010; 9:1678-88. [PMID: 20562411 PMCID: PMC2938060 DOI: 10.1074/mcp.r110.001461] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Indexed: 12/17/2022] Open
Abstract
To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e.g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe these parameters under physiological buffer conditions. With the atomic force microscope operating under such conditions, it is possible to obtain images of biological structures without requiring labeling and to follow dynamic processes in real time. Furthermore, by operating in force spectroscopy mode, it can probe intramolecular interactions and binding strengths. In structural biology, it has proven its ability to image proteins and protein conformational changes at submolecular resolution, and in proteomics, it is developing as a tool to map surface proteomes and to study protein function by force spectroscopy methods. The power of AFM to combine studies of protein form and protein function enables bridging various research fields to come to a comprehensive, molecular level picture of biological processes. We review the use of AFM imaging and force spectroscopy techniques and discuss the major advances of these experiments in further understanding form and function of proteins at the nanoscale in physiologically relevant environments.
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Affiliation(s)
- Marian Baclayon
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Wouter H. Roos
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Gijs J. L. Wuite
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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48
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Tertiary and secondary structure elasticity of a six-Ig titin chain. Biophys J 2010; 98:1085-95. [PMID: 20303866 DOI: 10.1016/j.bpj.2009.12.4192] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 11/25/2009] [Accepted: 12/02/2009] [Indexed: 12/11/2022] Open
Abstract
The protein titin functions as a mechanical spring conferring passive elasticity to muscle. Force spectroscopy studies have shown that titin exhibits several regimes of elasticity. Disordered segments bring about a soft, entropic spring-type elasticity; secondary structures of titin's immunoglobulin-like (Ig-) and fibronectin type III-like (FN-III) domains provide a stiff elasticity. In this study, we demonstrate a third type of elasticity due to tertiary structure and involving domain-domain interaction and reorganization along the titin chain. Through 870 ns of molecular dynamics simulations involving 29,000-635,000 atom systems, the mechanical properties of a six-Ig domain segment of titin (I65-I70), for which a crystallographic structure is available, are probed. The results reveal a soft tertiary structure elasticity. A remarkably accurate statistical mechanical description for this elasticity is derived and applied. Simulations also studied the stiff, secondary structure elasticity of the I65-I70 chain due to the unraveling of its domains and revealed how force propagates along the chain during the secondary structure elasticity response.
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49
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Linke WA, Krüger M. The Giant Protein Titin as an Integrator of Myocyte Signaling Pathways. Physiology (Bethesda) 2010; 25:186-98. [DOI: 10.1152/physiol.00005.2010] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The giant muscle protein titin, the “backbone” of the sarcomere, harbors a complex molecular spring whose stiffness is variably tuned in health and disease. Titin is increasingly recognized as a crucial integrator of diverse myocyte signaling pathways. The titin-associated signalosome includes hotspots of protein-protein interactions important for the regulation of protein quality-control mechanisms, hypertrophic gene activation, and mechanosensing.
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Affiliation(s)
- Wolfgang A. Linke
- Department of Cardiovascular Physiology, Institute of Physiology, Ruhr University Bochum, Bochum, Germany
| | - Martina Krüger
- Department of Cardiovascular Physiology, Institute of Physiology, Ruhr University Bochum, Bochum, Germany
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50
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Givli S. Towards multi-scale modeling of muscle fibers with sarcomere non-uniformities. J Theor Biol 2010; 264:882-92. [DOI: 10.1016/j.jtbi.2010.02.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 02/26/2010] [Accepted: 02/27/2010] [Indexed: 10/19/2022]
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