1
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Saini K, Cho S, Tewari M, Jalil AR, Wang M, Kasznel AJ, Yamamoto K, Chenoweth DM, Discher DE. Pan-tissue scaling of stiffness versus fibrillar collagen reflects contractility-driven strain that inhibits fibril degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559759. [PMID: 37808742 PMCID: PMC10557712 DOI: 10.1101/2023.09.27.559759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Polymer network properties such as stiffness often exhibit characteristic power laws in polymer density and other parameters. However, it remains unclear whether diverse animal tissues, composed of many distinct polymers, exhibit such scaling. Here, we examined many diverse tissues from adult mouse and embryonic chick to determine if stiffness ( E tissue ) follows a power law in relation to the most abundant animal protein, Collagen-I, even with molecular perturbations. We quantified fibrillar collagen in intact tissue by second harmonic generation (SHG) imaging and from tissue extracts by mass spectrometry (MS), and collagenase-mediated decreases were also tracked. Pan-tissue power laws for tissue stiffness versus Collagen-I levels measured by SHG or MS exhibit sub-linear scaling that aligns with results from cellularized gels of Collagen-I but not acellular gels. Inhibition of cellular myosin-II based contraction fits the scaling, and combination with inhibitors of matrix metalloproteinases (MMPs) show collagenase activity is strain - not stress- suppressed in tissues, consistent with past studies of gels and fibrils. Beating embryonic hearts and tendons, which differ in both collagen levels and stiffness by >1000-fold, similarly suppressed collagenases at physiological strains of ∼5%, with fiber-orientation regulating degradation. Scaling of E tissue based on 'use-it-or-lose-it' kinetics provides insight into scaling of organ size, microgravity effects, and regeneration processes while suggesting contractility-driven therapeutics.
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2
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Abraham Punnoose J, Thomas KJ, Chandrasekaran AR, Vilcapoma J, Hayden A, Kilpatrick K, Vangaveti S, Chen A, Banco T, Halvorsen K. High-throughput single-molecule quantification of individual base stacking energies in nucleic acids. Nat Commun 2023; 14:631. [PMID: 36746949 PMCID: PMC9902561 DOI: 10.1038/s41467-023-36373-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at -2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at -0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.
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Affiliation(s)
- Jibin Abraham Punnoose
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kevin J Thomas
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | | | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kacey Kilpatrick
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alan Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Thomas Banco
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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3
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Mechanochemistry of collagen. Acta Biomater 2023; 163:50-62. [PMID: 36669548 DOI: 10.1016/j.actbio.2023.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 01/02/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
The collagen molecular family is the result of nearly one billion years of evolution. It is a unique family of proteins, the majority of which provide general mechanical support to biological tissues. Fibril forming collagens are the most abundant collagens in vertebrate animals and are generally found in positions that resist tensile loading. In animals, cells produce fibril-forming collagen molecules that self-assemble into larger structures known as collagen fibrils. Collagen fibrils are the fundamental, continuous, load-bearing elements in connective tissues, but are often further aggregated into larger load-bearing structures, fascicles in tendon, lamellae in cornea and in intervertebral disk. We know that failure to form fibrillar collagen is embryonic lethal, and excessive collagen formation/growth (fibrosis) or uncontrolled enzymatic remodeling (type II collagen: osteoarthritis) is pathological. Collagen is thus critical to vertebrate viability and instrumental in maintaining efficient mechanical structures. However, despite decades of research, our understanding of collagen matrix formation is not complete, and we know still less about the detailed mechanisms that drive collagen remodeling, growth, and pathology. In this perspective, we examine the known role of mechanical force on the formation and development of collagenous structure. We then discuss a mechanochemical mechanism that has the potential to unify our understanding of collagenous tissue assembly dynamics, which preferentially deposits and grows collagen fibrils directly in the path of mechanical force, where the energetics should be dissuasive and where collagen fibrils are most required. We term this mechanism: Mechanochemical force-structure causality. STATEMENT OF SIGNIFICANCE: Our mechanochemical-force structure causality postulate suggests that collagen molecules are components of mechanochemically-sensitive and dynamically-responsive fibrils. Collagen molecules assemble preferentially in the path of applied strain, can be grown in place by mechanical extension, and are retained in the path of force through strain-stabilization. The mechanisms that drive this behavior operate at the level of the molecules themselves and are encoded into the structure of the biomaterial. The concept might change our understanding of structure formation, enhance our ability to treat injuries, and accelerate the development of therapeutics to prevent pathologies such as fibrosis. We suggest that collagen is a mechanochemically responsive dynamic element designed to provide a substantial "material assist" in the construction of adaptive carriers of mechanical signals.
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4
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Discovering design principles of collagen molecular stability using a genetic algorithm, deep learning, and experimental validation. Proc Natl Acad Sci U S A 2022; 119:e2209524119. [PMID: 36161946 DOI: 10.1073/pnas.2209524119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Collagen is the most abundant structural protein in humans, providing crucial mechanical properties, including high strength and toughness, in tissues. Collagen-based biomaterials are, therefore, used for tissue repair and regeneration. Utilizing collagen effectively during materials processing ex vivo and subsequent function in vivo requires stability over wide temperature ranges to avoid denaturation and loss of structure, measured as melting temperature (Tm). Although significant research has been conducted on understanding how collagen primary amino acid sequences correspond to Tm values, a robust framework to facilitate the design of collagen sequences with specific Tm remains a challenge. Here, we develop a general model using a genetic algorithm within a deep learning framework to design collagen sequences with specific Tm values. We report 1,000 de novo collagen sequences, and we show that we can efficiently use this model to generate collagen sequences and verify their Tm values using both experimental and computational methods. We find that the model accurately predicts Tm values within a few degrees centigrade. Further, using this model, we conduct a high-throughput study to identify the most frequently occurring collagen triplets that can be directly incorporated into collagen. We further discovered that the number of hydrogen bonds within collagen calculated with molecular dynamics (MD) is directly correlated to the experimental measurement of triple-helical quality. Ultimately, we see this work as a critical step to helping researchers develop collagen sequences with specific Tm values for intended materials manufacturing methods and biomedical applications, realizing a mechanistic materials by design paradigm.
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5
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Optimization of a Calcium-Based Treatment Method for Jellyfish to Design Food for the Future. Foods 2022; 11:foods11172697. [PMID: 36076882 PMCID: PMC9455609 DOI: 10.3390/foods11172697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Edible jellyfish are a traditional Southeast Asian food, usually prepared as a rehydrated product using a salt and alum mixture, whereas they are uncommon in Western Countries and considered as a novel food in Europe. Here, a recently developed, new approach for jellyfish processing and stabilization with calcium salt brining was upgraded by modifying the pre-treatment step of freshly caught jellyfish and successfully applied to several edible species. Treated jellyfish obtained by the application of the optimized version of this method respected both quality and safety parameters set by EU law, including no pathogenic microorganisms, absence or negligible levels of histamine and of total volatile basic nitrogen, no heavy metals; and the total bacterial, yeast, and mold counts were either negligible or undetectable. Jellyfish treated by the presented method exhibited unique protein content, amino acid and fatty acid profiles, antioxidant activity, and texture. The optimized method, initially set up on Rhiszostoma pulmo, was also successfully applied to other edible jellyfish species (such as Cotylorhiza tuberculata, Phyllorhiza punctata, and Rhopilema nomadica) present in the Mediterranean Sea. This study discloses an innovative process for the preparation of jellyfish-based food products for potential future distribution in Europe.
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6
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Pokhrel P, Hu C, Mao H. Ensemble Force Spectroscopy by Shear Forces. J Vis Exp 2022:10.3791/63741. [PMID: 35969056 PMCID: PMC10373445 DOI: 10.3791/63741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Single-molecule techniques based on fluorescence and mechanochemical principles provide superior sensitivity in biological sensing. However, due to the lack of high throughput capabilities, the application of these techniques is limited in biophysics. Ensemble force spectroscopy (EFS) has demonstrated high throughput in the investigation of a massive set of molecular structures by converting mechanochemical studies of individual molecules into those of molecular ensembles. In this protocol, the DNA secondary structures (i-motifs) were unfolded in the shear flow between the rotor and stator of a homogenizer tip at shear rates up to 77796/s. The effects of flow rates and molecular sizes on the shear forces experienced by the i-motif were demonstrated. The EFS technique also revealed the binding affinity between DNA i-motifs and ligands. Furthermore, we have demonstrated a click chemistry reaction that can be actuated by shear force (i.e., mechano-click chemistry). These results establish the effectiveness of using shear force to control the conformation of molecular structures.
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Affiliation(s)
- Pravin Pokhrel
- Department of Chemistry & Biochemistry, Kent State University
| | - Changpeng Hu
- Department of Chemistry & Biochemistry, Kent State University
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University;
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7
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Al-Shaer A, Lyons A, Ishikawa Y, Hudson BG, Boudko SP, Forde NR. Sequence-dependent mechanics of collagen reflect its structural and functional organization. Biophys J 2021; 120:4013-4028. [PMID: 34390685 DOI: 10.1016/j.bpj.2021.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/25/2021] [Accepted: 08/06/2021] [Indexed: 01/06/2023] Open
Abstract
Extracellular matrix mechanics influence diverse cellular functions, yet surprisingly little is known about the mechanical properties of their constituent collagen proteins. In particular, network-forming collagen IV, an integral component of basement membranes, has been far less studied than fibril-forming collagens. A key feature of collagen IV is the presence of interruptions in the triple-helix-defining (Gly-X-Y) sequence along its collagenous domain. Here, we used atomic force microscopy to determine the impact of sequence heterogeneity on the local flexibility of collagen IV and of the fibril-forming collagen III. Our extracted flexibility profile of collagen IV reveals that it possesses highly heterogeneous mechanics, ranging from semiflexible regions as found for fibril-forming collagens to a lengthy region of high flexibility toward its N-terminus. A simple model in which flexibility is dictated only by the presence of interruptions fit the extracted profile reasonably well, providing insight into the alignment of chains and demonstrating that interruptions, particularly when coinciding in multiple chains, significantly enhance local flexibility. To a lesser extent, sequence variations within the triple helix lead to variable flexibility, as seen along the continuously triple-helical collagen III. We found this fibril-forming collagen to possess a high-flexibility region around its matrix-metalloprotease binding site, suggesting a unique mechanical fingerprint of this region that is key for matrix remodeling. Surprisingly, proline content did not correlate with local flexibility in either collagen type. We also found that physiologically relevant changes in pH and chloride concentration did not alter the flexibility of collagen IV, indicating such environmental changes are unlikely to control its compaction during secretion. Although extracellular chloride ions play a role in triggering collagen IV network formation, they do not appear to modulate the structure of its collagenous domain.
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Affiliation(s)
- Alaa Al-Shaer
- Department of Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada
| | - Aaron Lyons
- Department of Physics, Burnaby, British Columbia, Canada
| | - Yoshihiro Ishikawa
- Department of Ophthalmology, University of California San Francisco, School of Medicine, San Francisco, California
| | - Billy G Hudson
- Department of Medicine, Division of Nephrology and Hypertension, Nashville, Tennessee; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biochemistry, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Nashville, Tennessee; Department of Cell and Developmental Biology, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee
| | - Sergei P Boudko
- Department of Medicine, Division of Nephrology and Hypertension, Nashville, Tennessee; Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Biochemistry, Nashville, Tennessee
| | - Nancy R Forde
- Department of Molecular Biology and Biochemistry, Burnaby, British Columbia, Canada; Department of Physics, Burnaby, British Columbia, Canada; Department of Chemistry, Burnaby, British Columbia, Canada; Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, British Columbia, Canada.
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8
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Hu C, Jonchhe S, Pokhrel P, Karna D, Mao H. Mechanical unfolding of ensemble biomolecular structures by shear force. Chem Sci 2021; 12:10159-10164. [PMID: 34377405 PMCID: PMC8336480 DOI: 10.1039/d1sc02257a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/11/2021] [Indexed: 01/09/2023] Open
Abstract
Mechanical unfolding of biomolecular structures has been exclusively performed at the single-molecule level by single-molecule force spectroscopy (SMFS) techniques. Here we transformed sophisticated mechanical investigations on individual molecules into a simple platform suitable for molecular ensembles. By using shear flow inside a homogenizer tip, DNA secondary structures such as i-motifs are unfolded by shear force up to 50 pN at a 77 796 s-1 shear rate. We found that the larger the molecules, the higher the exerted shear forces. This shear force approach revealed affinity between ligands and i-motif structures. It also demonstrated a mechano-click reaction in which a Cu(i) catalyzed azide-alkyne cycloaddition was modulated by shear force. We anticipate that this ensemble force spectroscopy method can investigate intra- and inter-molecular interactions with the throughput, accuracy, and robustness unparalleled to those of SMFS methods.
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Affiliation(s)
- Changpeng Hu
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Advanced Materials and Liquid Crystal Institute, Kent State University Kent OH 44242 USA
| | - Sagun Jonchhe
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Advanced Materials and Liquid Crystal Institute, Kent State University Kent OH 44242 USA
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Advanced Materials and Liquid Crystal Institute, Kent State University Kent OH 44242 USA
| | - Deepak Karna
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Advanced Materials and Liquid Crystal Institute, Kent State University Kent OH 44242 USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Advanced Materials and Liquid Crystal Institute, Kent State University Kent OH 44242 USA
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9
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Abraham Punnoose J, Hayden A, Zhou L, Halvorsen K. Wi-Fi Live-Streaming Centrifuge Force Microscope for Benchtop Single-Molecule Experiments. Biophys J 2020; 119:2231-2239. [PMID: 33121943 PMCID: PMC7732769 DOI: 10.1016/j.bpj.2020.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 11/21/2022] Open
Abstract
The ability to apply controlled forces to individual molecules has been revolutionary in shaping our understanding of biophysics in areas as diverse as dynamic bond strength, biological motor operation, and DNA replication. However, the methodology to perform single-molecule experiments remains relatively inaccessible because of cost and complexity. In 2010, we introduced the centrifuge force microscope (CFM) as a platform for accessible and high-throughput single-molecule experimentation. The CFM consists of a rotating microscope with which prescribed centrifugal forces can be applied to microsphere-tethered biomolecules. In this work, we develop and demonstrate a next-generation Wi-Fi CFM that offers unprecedented ease of use and flexibility in design. The modular CFM unit fits within a standard benchtop centrifuge and connects by Wi-Fi to an external computer for live control and streaming at near gigabit speeds. The use of commercial wireless hardware allows for flexibility in programming and provides a streamlined upgrade path as Wi-Fi technology advances. To facilitate ease of use, detailed build and setup instructions, as well as LabVIEW-based control software and MATLAB-based analysis software, are provided. We demonstrate the instrument’s performance by analysis of force-dependent dissociation of short DNA duplexes of 7, 8, and 9 bp. We showcase the sensitivity of the approach by resolving distinct dissociation kinetic rates for a 7 bp duplex in which one G-C basepair is mutated to an A-T basepair.
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Affiliation(s)
| | | | - Lifeng Zhou
- RNA Institute, SUNY at Albany, Albany, New York
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10
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Lehmann K, Shayegan M, Blab GA, Forde NR. Optical Tweezers Approaches for Probing Multiscale Protein Mechanics and Assembly. Front Mol Biosci 2020; 7:577314. [PMID: 33134316 PMCID: PMC7573139 DOI: 10.3389/fmolb.2020.577314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
Multi-step assembly of individual protein building blocks is key to the formation of essential higher-order structures inside and outside of cells. Optical tweezers is a technique well suited to investigate the mechanics and dynamics of these structures at a variety of size scales. In this mini-review, we highlight experiments that have used optical tweezers to investigate protein assembly and mechanics, with a focus on the extracellular matrix protein collagen. These examples demonstrate how optical tweezers can be used to study mechanics across length scales, ranging from the single-molecule level to fibrils to protein networks. We discuss challenges in experimental design and interpretation, opportunities for integration with other experimental modalities, and applications of optical tweezers to current questions in protein mechanics and assembly.
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Affiliation(s)
- Kathrin Lehmann
- Department of Physics, Simon Fraser University, Burnaby, BC, Canada.,Soft Condensed Matter and Biophysics, Utrecht University, Utrecht, Netherlands
| | - Marjan Shayegan
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Gerhard A Blab
- Soft Condensed Matter and Biophysics, Utrecht University, Utrecht, Netherlands
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada.,Centre for Cell Biology, Development and Disease (C2D2), Simon Fraser University, Burnaby, BC, Canada
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11
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Abstract
Many proteins in cells and in the extracellular matrix assemble into force-bearing networks, and some proteins clearly transduce mechanical stimuli into biochemical signals. Although structural mechanisms remain poorly understood, the designs of such proteins enable mechanical forces to either inhibit or facilitate interactions of protein domains with other proteins, including small molecules and enzymes, including proteases and kinases. Here, we review some of the structural proteins and processes that exhibit distinct modes of force-dependent signal conversion.
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Affiliation(s)
- Karanvir Saini
- Molecular and Cell Biophysics Lab , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Dennis E Discher
- Molecular and Cell Biophysics Lab , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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12
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Kirkness MWH, Lehmann K, Forde NR. Mechanics and structural stability of the collagen triple helix. Curr Opin Chem Biol 2019; 53:98-105. [DOI: 10.1016/j.cbpa.2019.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/24/2019] [Accepted: 08/12/2019] [Indexed: 01/18/2023]
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13
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Iqbal SMA, Deska-Gauthier D, Kreplak L. Assessing collagen fibrils molecular damage after a single stretch-release cycle. SOFT MATTER 2019; 15:6237-6246. [PMID: 31334527 DOI: 10.1039/c9sm00832b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mechanical testing of connective tissues such as tendons and ligaments can lead to collagen denaturation even in the absence of macroscale damage. The following tensile loading protocols, ramp loading to failure, overloading and release, cyclic overloading and cyclic fatigue loading, all yield molecular damage in rat or bovine tendons. Single collagen fibrils extracted from the positional common digital extensor tendon of the forelimb also show molecular damage after tensile loading to failure. Using fibrils from the same source we assess changes to the molecular and supramolecular structure after tensile stress relaxation at strains between 4 and 22% followed by release. We observe no broken fibril and no significant change in D-band spacing. However, we observe significant binding of a fluorescent collagen hybridizing peptide to the fibrils indicating that collagen denaturation occurs in a strain dependent way for relaxation times between 1 s and 1500 s. We also show that peptide binding is associated with a decrease of the cross-sectional area of the fibrils providing an estimate of the dry volume loss due to molecular denaturation as well as an estimate of the mechanical energy density required, 25-110 MJ m-3. In summary we show that collagen molecular damage can occur in the absence of fibril failure and without visible changes to the supramolecular structure.
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Affiliation(s)
- S M Asif Iqbal
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Canada.
| | | | - Laurent Kreplak
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Canada. and School of Biomedical Engineering, Dalhousie University, Halifax, Canada
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14
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Tension in fibrils suppresses their enzymatic degradation - A molecular mechanism for 'use it or lose it'. Matrix Biol 2019; 85-86:34-46. [PMID: 31201857 DOI: 10.1016/j.matbio.2019.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 12/27/2022]
Abstract
Tissue homeostasis depends on a balance of synthesis and degradation of constituent proteins, with turnover of a given protein potentially regulated by its use. Extracellular matrix (ECM) is predominantly composed of fibrillar collagens that exhibit tension-sensitive degradation, which we review here at different levels of hierarchy. Past experiments and recent proteomics measurements together suggest that mechanical strain stabilizes collagen against enzymatic degradation at the scale of tissues and fibrils whereas isolated collagen molecules exhibit a biphasic behavior that depends on load magnitude. Within a Michaelis-Menten framework, collagenases at constant concentration effectively exhibit a low activity on substrate fibrils when the fibrils are strained by tension. Mechanisms of such mechanosensitive regulation are surveyed together with relevant interactions of collagen fibrils with cells.
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15
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Drabek AA, Loparo JJ, Blacklow SC. A Flow-Extension Tethered Particle Motion Assay for Single-Molecule Proteolysis. Biochemistry 2019; 58:2509-2518. [PMID: 30946563 PMCID: PMC6607913 DOI: 10.1021/acs.biochem.9b00106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Regulated proteolysis of signaling proteins under mechanical tension enables cells to communicate with their environment in a variety of developmental and physiologic contexts. The role of force in inducing proteolytic sensitivity has been explored using magnetic tweezers at the single-molecule level with bead-tethered assays, but such efforts have been limited by challenges in ensuring that beads not be restrained by multiple tethers. Here, we describe a multiplexed assay for single-molecule proteolysis that overcomes the multiple-tether problem using a flow-extension strategy on a microscope equipped with magnetic tweezers. Particle tracking and computational sorting of flow-induced displacements allow assignment of tethered substrates to singly captured and multiply tethered bins, with the fraction of fully mobile, single-tether substrates depending inversely on the concentration of substrate loaded on the coverslip. Computational exclusion of multiple-tether beads enables robust assessment of on-target proteolysis by the highly specific tobacco etch virus protease and the more promiscuous metalloprotease ADAM17. This method should be generally applicable to a wide range of proteases and readily extensible to robust evaluation of proteolytic sensitivity as a function of applied magnetic force.
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Affiliation(s)
- Andrew A. Drabek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J. Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stephen C. Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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16
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Croop B, Han KY. Facile single-molecule pull-down assay for analysis of endogenous proteins. Phys Biol 2019; 16:035002. [PMID: 30769341 DOI: 10.1088/1478-3975/ab0792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The single-molecule pull-down (SiMPull) assay analyzes molecular complexes in physiological conditions from cell or tissue lysates. Currently the approach requires a lengthy sample preparation process, which has largely prevented the widespread adoption of this technique in bioanalysis. Here, we present a simplified SiMPull assay based upon dichlorodimethylsilane-Tween-20 passivation and F(ab) fragment labeling. Our passivation is a much shorter process than the standard polyethylene glycol passivation used in most single-molecule studies. The use of F(ab) fragments for indirect fluorescent labeling rather than divalent F(ab')2 or whole IgG antibodies allows for the pre-incubation of the detection antibodies, reducing the sample preparation time for single-molecule immunoprecipitation samples. We examine the applicability of our approach to recombinant proteins and endogenous proteins from mammalian cell lysates.
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Affiliation(s)
- Benjamin Croop
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, United States of America
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17
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Nathwani B, Shih WM, Wong WP. Force Spectroscopy and Beyond: Innovations and Opportunities. Biophys J 2018; 115:2279-2285. [PMID: 30447991 PMCID: PMC6302248 DOI: 10.1016/j.bpj.2018.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 10/08/2018] [Accepted: 10/25/2018] [Indexed: 12/26/2022] Open
Abstract
Life operates at the intersection of chemistry and mechanics. Over the years, we have made remarkable progress in understanding life from a biochemical perspective and the mechanics of life at the single-molecule scale. Yet the full integration of physical and mechanical models into mainstream biology has been impeded by technical and conceptual barriers, including limitations in our ability to 1) easily measure and apply mechanical forces to biological systems, 2) scale these measurements from single-molecule characterization to more complex biomolecular systems, and 3) model and interpret biophysical data in a coherent way across length scales that span single molecules to cells to multicellular organisms. In this manuscript, through a look at historical and recent developments in force spectroscopy techniques and a discussion of a few exemplary open problems in cellular biomechanics, we aim to identify research opportunities that will help us reach our goal of a more complete and integrated understanding of the role of force and mechanics in biological systems.
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Affiliation(s)
- Bhavik Nathwani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts.
| | - William M Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts
| | - Wesley P Wong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts.
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Kirkness MWH, Korosec CS, Forde NR. Modified Pluronic F127 Surface for Bioconjugation and Blocking Nonspecific Adsorption of Microspheres and Biomacromolecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:13550-13557. [PMID: 30303387 DOI: 10.1021/acs.langmuir.8b02877] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many experiments and applications require the chemical coupling of target molecules to surfaces, during which the elimination of nonspecific interactions presents a difficult challenge. We report on a technologically accessible surface passivation and chemical conjugation method based on an NHS end-labeled F127 Pluronic block copolymer (F127-NHS). To quantify interactions between the F127-NHS surface and magnetic microspheres, we developed a simple assay: the microsphere adhesion by gravity, inversion, then counting, or "MAGIC" assay. To improve blocking of microspheres while maintaining the ability to chemically couple additional molecules, we implemented a pH-dependent two-step chemical modification process for amine microspheres. This process achieves an extremely high level of blocking nonspecific interactions (less than 2% nonspecific adhesion) for a variety of microsphere surface charges and chemical functionalities. We also demonstrate the ability to specifically tether magnetic microspheres to an F127-NHS surface, using single DNA molecules. Using the DNA microspheres, we establish the applicability of the surface for force spectroscopy (stable with an applied load >30 pN) via the massively parallel technique of centrifuge force microscopy. Finally, we demonstrate that the surface can be used in fluorescence studies with a fluorogenic peptide cleavage assay, with high levels of blocking achieved for both the fluorogenic peptide and trypsin. These results suggest applications including, but not limited to, single-molecule force spectroscopy and fluorescence, biosensors, medical implants, and anti-biofouling, which could make use of the F127-NHS surface.
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Rezaei N, Lyons A, Forde NR. Environmentally Controlled Curvature of Single Collagen Proteins. Biophys J 2018; 115:1457-1469. [PMID: 30269884 PMCID: PMC6260212 DOI: 10.1016/j.bpj.2018.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/02/2018] [Accepted: 09/04/2018] [Indexed: 12/01/2022] Open
Abstract
The predominant structural protein in vertebrates is collagen, which plays a key role in extracellular matrix and connective tissue mechanics. Despite its prevalence and physical importance in biology, the mechanical properties of molecular collagen are far from established. The flexibility of its triple helix is unresolved, with descriptions from different experimental techniques ranging from flexible to semirigid. Furthermore, it is unknown how collagen type (homo- versus heterotrimeric) and source (tissue derived versus recombinant) influence flexibility. Using SmarTrace, a chain-tracing algorithm we devised, we performed statistical analysis of collagen conformations collected with atomic force microscopy to determine the protein's mechanical properties. Our results show that types I, II, and III collagens-the key fibrillar varieties-exhibit similar molecular flexibilities. However, collagen conformations are strongly modulated by salt, transitioning from compact to extended as KCl concentration increases in both neutral and acidic pH. Although analysis with a standard worm-like chain model suggests that the persistence length of collagen can attain a wide range of values within the literature range, closer inspection reveals that this modulation of collagen's conformational behavior is not due to changes in flexibility but rather arises from the induction of curvature (either intrinsic or induced by interactions with the mica surface). By modifying standard polymer theory to include innate curvature, we show that collagen behaves as an equilibrated curved worm-like chain in two dimensions. Analysis within the curved worm-like chain model shows that collagen's curvature depends strongly on pH and salt, whereas its persistence length does not. Thus, we find that triple-helical collagen is well described as semiflexible irrespective of source, type, pH, and salt environment. These results demonstrate that collagen is more flexible than its conventional description as a rigid rod, which may have implications for its cellular processing and secretion.
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Affiliation(s)
- Nagmeh Rezaei
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Aaron Lyons
- Department of Physics, Simon Fraser University, Burnaby, Canada
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, Canada.
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Unlocking Collagen Proteolysis with a Gentle Pull. Biophys J 2018; 114:503-504. [PMID: 29414694 DOI: 10.1016/j.bpj.2017.11.3788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/02/2017] [Indexed: 11/21/2022] Open
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