1
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Liu Y, Song D, Li S, Guo Z, Zheng P. Click Chemistry-Based Force Spectroscopy Revealed Enhanced Binding Dynamics of Phosphorylated HMGB1 to Cisplatin-DNA. J Am Chem Soc 2024; 146:13126-13132. [PMID: 38696488 DOI: 10.1021/jacs.4c00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Cisplatin, a cornerstone in cancer chemotherapy, is known for its DNA-binding capacity and forms lesions that lead to cancer cell death. However, the repair of these lesions compromises cisplatin's effectiveness. This study investigates how phosphorylation of HMGB1, a nuclear protein, modifies its binding to cisplatin-modified DNA (CP-DNA) and thus protects it from repair. Despite numerous methods for detecting protein-DNA interactions, quantitative approaches for understanding their molecular mechanism remain limited. Here, we applied click chemistry-based single-molecule force spectroscopy, achieving high-precision quantification of the interaction between phosphorylated HMGB1 and CP-DNA. This method utilizes a synergy of click chemistry and enzymatic ligation for precise DNA-protein immobilization and interaction in the system. Our results revealed that HMGB1 binds to CP-DNA with a significantly high rupture force of ∼130 pN, stronger than most natural DNA-protein interactions and varying across different DNA sequences. Moreover, Ser14 is identified as the key phosphorylation site, enhancing the interaction's kinetic stability by 35-fold. This increase in stability is attributed to additional hydrogen bonding suggested by molecular dynamics (MD) simulations. Our findings not only reveal the important role of phosphorylated HMGB1 in potentially improving cisplatin's therapeutic efficacy but also provide a precise method for quantifying protein-DNA interactions.
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Affiliation(s)
- Yutong Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Senmiao Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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2
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Wang W, An Z, Wang Z, Wang S. Chemical Design of Supramolecular Reversible Adhesives for Promising Applications. Chemistry 2024; 30:e202304349. [PMID: 38308610 DOI: 10.1002/chem.202304349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/05/2024]
Abstract
Supramolecular reversible adhesives have garnered significant attention due to their potential applications in various fields. These adhesives exhibit remarkable properties such as reversible adhesion, self-healing, and high flexibility. This concept aims to present a comprehensive overview of the current research progress in developing supramolecular reversible adhesives. Firstly, the fundamentals of supramolecular chemistry and the principles underlying the design and synthesis of reversible adhesive systems are discussed. Next, the concept focuses on characterizing the reversible adhesion strength of supramolecular adhesive systems that have been developed. The adhesion performance of supramolecular reversible adhesives is summarized, highlighting their unique characteristics and promising applications. Finally, the challenges and future perspectives in the field of supramolecular reversible adhesives are discussed. The comprehensive overview provided in this concept aims to inspire further research and innovation in this exciting field.
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Affiliation(s)
- Wenbo Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zixin An
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhao Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Shutao Wang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, Jiangsu, 215123, P. R. China
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3
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Doyle LA, Takushi B, Kibler RD, Milles LF, Orozco CT, Jones JD, Jackson SE, Stoddard BL, Bradley P. De novo design of knotted tandem repeat proteins. Nat Commun 2023; 14:6746. [PMID: 37875492 PMCID: PMC10598012 DOI: 10.1038/s41467-023-42388-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (31) and pentafoil (51) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein's structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.
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Affiliation(s)
- Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Brittany Takushi
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Carolina T Orozco
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Jonathan D Jones
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sophie E Jackson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
| | - Philip Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. North, Seattle, WA, 98109, USA.
- Division of Public Health Sciences and Program in Computational Biology, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N, Seattle, WA, 98009, USA.
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4
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dos Santos Natividade R, Koehler M, Gomes PSFC, Simpson JD, Smith SC, Gomes DEB, de Lhoneux J, Yang J, Ray A, Dermody TS, Bernardi RC, Ogden KM, Alsteens D. Deciphering molecular mechanisms stabilizing the reovirus-binding complex. Proc Natl Acad Sci U S A 2023; 120:e2220741120. [PMID: 37186838 PMCID: PMC10214207 DOI: 10.1073/pnas.2220741120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Mammalian orthoreoviruses (reoviruses) serve as potential triggers of celiac disease and have oncolytic properties, making these viruses potential cancer therapeutics. Primary attachment of reovirus to host cells is mainly mediated by the trimeric viral protein, σ1, which engages cell-surface glycans, followed by high-affinity binding to junctional adhesion molecule-A (JAM-A). This multistep process is thought to be accompanied by major conformational changes in σ1, but direct evidence is lacking. By combining biophysical, molecular, and simulation approaches, we define how viral capsid protein mechanics influence virus-binding capacity and infectivity. Single-virus force spectroscopy experiments corroborated by in silico simulations show that GM2 increases the affinity of σ1 for JAM-A by providing a more stable contact interface. We demonstrate that conformational changes in σ1 that lead to an extended rigid conformation also significantly increase avidity for JAM-A. Although its associated lower flexibility impairs multivalent cell attachment, our findings suggest that diminished σ1 flexibility enhances infectivity, indicating that fine-tuning of σ1 conformational changes is required to successfully initiate infection. Understanding properties underlying the nanomechanics of viral attachment proteins offers perspectives in the development of antiviral drugs and improved oncolytic vectors.
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Affiliation(s)
- Rita dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354Freising, Germany
| | | | - Joshua D. Simpson
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Sydni Caet Smith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 37232Nashville, TN
| | | | - Juliette de Lhoneux
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Terence S. Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA15213
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center, Children’s Hospital of Pittsburgh, Pittsburgh, PA15213
| | | | - Kristen M. Ogden
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 37232Nashville, TN
- Department of Pediatrics, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN37232
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
- Walloon Excellence in Life sciences and Biotechnology, Walloon Excellence Research Institute, 1300Wavre, Belgium
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5
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Gomes PSFC, Forrester M, Pace M, Gomes DEB, Bernardi RC. May the force be with you: The role of hyper-mechanostability of the bone sialoprotein binding protein during early stages of Staphylococci infections. Front Chem 2023; 11:1107427. [PMID: 36846849 PMCID: PMC9944720 DOI: 10.3389/fchem.2023.1107427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
The bone sialoprotein-binding protein (Bbp) is a mechanoactive MSCRAMM protein expressed on the surface of Staphylococcus aureus that mediates adherence of the bacterium to fibrinogen-α (Fgα), a component of the bone and dentine extracellular matrix of the host cell. Mechanoactive proteins like Bbp have key roles in several physiological and pathological processes. Particularly, the Bbp: Fgα interaction is important in the formation of biofilms, an important virulence factor of pathogenic bacteria. Here, we investigated the mechanostability of the Bbp: Fgα complex using in silico single-molecule force spectroscopy (SMFS), in an approach that combines results from all-atom and coarse-grained steered molecular dynamics (SMD) simulations. Our results show that Bbp is the most mechanostable MSCRAMM investigated thus far, reaching rupture forces beyond the 2 nN range in typical experimental SMFS pulling rates. Our results show that high force-loads, which are common during initial stages of bacterial infection, stabilize the interconnection between the protein's amino acids, making the protein more "rigid". Our data offer new insights that are crucial on the development of novel anti-adhesion strategies.
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Affiliation(s)
- Priscila S. F. C. Gomes
- Department of Physics, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Meredith Forrester
- Department of Physics, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Margaret Pace
- Department of Physics, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
| | - Diego E. B. Gomes
- Department of Physics, College of Sciences and Mathematics, Auburn University, Auburn, AL, United States
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6
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Apostolidou D, Zhang P, Yang W, Marszalek PE. Mechanical Unfolding and Refolding of NanoLuc via Single-Molecule Force Spectroscopy and Computer Simulations. Biomacromolecules 2022; 23:5164-5178. [PMID: 36350253 DOI: 10.1021/acs.biomac.2c00997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A highly bioluminescent protein, NanoLuc (Nluc), has seen numerous applications in biological assays since its creation. We recently engineered a NanoLuc polyprotein that showed high bioluminescence but displayed a strong misfolding propensity after mechanical unfolding. Here, we present our single-molecule force spectroscopy (SMFS) studies by atomic force microscopy (AFM) and steered molecular dynamics (SMD) simulations on two new hybrid protein constructs comprised of Nluc and I91 titin domains, I91-I91-Nluc-I91-I91-I91-I91 (I912-Nluc-I914) and I91-Nluc-I91-Nluc-I91-Nluc-I91, to characterize the unfolding behavior of Nluc in detail and to further investigate its misfolding properties that we observed earlier for the I912-Nluc3-I912 construct. Our SMFS results confirm that Nluc's unfolding proceeds similarly in all constructs; however, Nluc's refolding differs in these constructs, and its misfolding is minimized when Nluc is monomeric or separated by I91 domains. Our simulations on monomeric Nluc, Nluc dyads, and Nluc triads pinpointed the origin of its mechanical stability and captured interesting unfolding intermediates, which we also observed experimentally.
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Affiliation(s)
- Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27708, United States
| | - Pan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina27708, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina27708, United States
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7
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Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules. Proc Natl Acad Sci U S A 2022; 119:e2117467119. [PMID: 36215467 PMCID: PMC9586272 DOI: 10.1073/pnas.2117467119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein-carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM-substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose-CBM bond rupture forces exceeding 15 pN.
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8
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Gomes PSFC, Gomes DEB, Bernardi RC. Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy. FRONTIERS IN BIOINFORMATICS 2022; 2:983306. [PMID: 36304287 PMCID: PMC9580946 DOI: 10.3389/fbinf.2022.983306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Mechanoactive proteins are essential for a myriad of physiological and pathological processes. Guided by the advances in single-molecule force spectroscopy (SMFS), we have reached a molecular-level understanding of how mechanoactive proteins sense and respond to mechanical forces. However, even SMFS has its limitations, including the lack of detailed structural information during force-loading experiments. That is where molecular dynamics (MD) methods shine, bringing atomistic details with femtosecond time-resolution. However, MD heavily relies on the availability of high-resolution structural data, which is not available for most proteins. For instance, the Protein Data Bank currently has 192K structures deposited, against 231M protein sequences available on Uniprot. But many are betting that this gap might become much smaller soon. Over the past year, the AI-based AlphaFold created a buzz on the structural biology field by being able to predict near-native protein folds from their sequences. For some, AlphaFold is causing the merge of structural biology with bioinformatics. Here, using an in silico SMFS approach pioneered by our group, we investigate how reliable AlphaFold structure predictions are to investigate mechanical properties of Staphylococcus bacteria adhesins proteins. Our results show that AlphaFold produce extremally reliable protein folds, but in many cases is unable to predict high-resolution protein complexes accurately. Nonetheless, the results show that AlphaFold can revolutionize the investigation of these proteins, particularly by allowing high-throughput scanning of protein structures. Meanwhile, we show that the AlphaFold results need to be validated and should not be employed blindly, with the risk of obtaining an erroneous protein mechanism.
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9
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Shi S, Wu T, Zheng P. Direct Measurements of the Cobalt-thiolate Bonds Strength in Rubredoxin by Single-Molecule Force Spectroscopy. Chembiochem 2022; 23:e202200165. [PMID: 35475313 DOI: 10.1002/cbic.202200165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/26/2022] [Indexed: 11/07/2022]
Abstract
Cobalt is a trace transition metal. Although it is not abundant on earth, tens of cobalt-containing proteins exist in life. Moreover, the characteristic spectrum of Co(II) ion makes it a powerful probe for the characterization of metal-binding proteins through the formation of cobalt-ligand bonds. Since most of these natural and artificial cobalt-containing proteins are stable, we believe that these cobalt-ligand bonds in the protein system are also mechanically stable. To prove this, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to directly measure the rupture force of Co(II)-thiolate bond in Co-substituted rubredoxin (CoRD). By combining the chemical denature/renature method for building metalloprotein and cysteine coupling-based polyprotein construction strategy, we successfully prepared the polyprotein sample (CoRD) n suitable for single-molecule study. Thus, we quantified the strength of Co(II)-thiolate bonds in rubredoxin with a rupture force of ~140 pN, revealing that the bond is a stable chemical bond. In addition, the Co-S bond is more labile than the Zn-S bond in proteins, similar to the result from the metal-competing titration experiment.
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Affiliation(s)
- Shengchao Shi
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Tao Wu
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Peng Zheng
- Nanjing University, School of Chemistry and Chemical Engineering, 168 Xianlin Ave, Nanjing, Jiangsu Province, 210023, Nanjing, CHINA
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10
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Dong Y, Lin W, Laaksonen A, Ji X. Complementary Powerful Techniques for Investigating the Interactions of Proteins with Porous TiO2 and Its Hybrid Materials: A Tutorial Review. MEMBRANES 2022; 12:membranes12040415. [PMID: 35448385 PMCID: PMC9029952 DOI: 10.3390/membranes12040415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022]
Abstract
Understanding the adsorption and interaction between porous materials and protein is of great importance in biomedical and interface sciences. Among the studied porous materials, TiO2 and its hybrid materials, featuring distinct, well-defined pore sizes, structural stability and excellent biocompatibility, are widely used. In this review, the use of four powerful, synergetic and complementary techniques to study protein-TiO2-based porous materials interactions at different scales is summarized, including high-performance liquid chromatography (HPLC), atomic force microscopy (AFM), surface-enhanced Raman scattering (SERS), and Molecular Dynamics (MD) simulations. We expect that this review could be helpful in optimizing the commonly used techniques to characterize the interfacial behavior of protein on porous TiO2 materials in different applications.
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Affiliation(s)
- Yihui Dong
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel;
- Correspondence: (Y.D.); (X.J.)
| | - Weifeng Lin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Aatto Laaksonen
- Energy Engineering, Division of Energy Science, Luleå University of Technology, 97187 Luleå, Sweden;
- Arrhenius Laboratory, Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
- Center of Advanced Research in Bionanoconjugates and Biopolymers, ‘‘Petru Poni” Institute of Macromolecular Chemistry, 700469 Iasi, Romania
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xiaoyan Ji
- Energy Engineering, Division of Energy Science, Luleå University of Technology, 97187 Luleå, Sweden;
- Correspondence: (Y.D.); (X.J.)
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11
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Abstract
In the dynamic environment of the airways, where SARS-CoV-2 infections are initiated by binding to human host receptor ACE2, mechanical stability of the viral attachment is a crucial fitness advantage. Using single-molecule force spectroscopy techniques, we mimic the effect of coughing and sneezing, thereby testing the force stability of SARS-CoV-2 RBD:ACE2 interaction under physiological conditions. Our results reveal a higher force stability of SARS-CoV-2 binding to ACE2 compared to SARS-CoV-1, causing a possible fitness advantage. Our assay is sensitive to blocking agents preventing RBD:ACE2 bond formation. It will thus provide a powerful approach to investigate the modes of action of neutralizing antibodies and other agents designed to block RBD binding to ACE2 that are currently developed as potential COVID-19 therapeutics. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are initiated by attachment of the receptor-binding domain (RBD) on the viral Spike protein to angiotensin-converting enzyme-2 (ACE2) on human host cells. This critical first step occurs in dynamic environments, where external forces act on the binding partners and avidity effects play an important role, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using magnetic tweezers and atomic force spectroscopy as highly complementary single-molecule force spectroscopy techniques, we investigate the RBD:ACE2 interaction over the whole physiologically relevant force range. We combine the experimental results with steered molecular dynamics simulations and observe and assign fully consistent unbinding and unfolding events across the three techniques, enabling us to establish ACE2 unfolding as a molecular fingerprint. Measuring at forces of 2 to 5 pN, we quantify the force dependence and kinetics of the RBD:ACE2 bond in equilibrium. We show that the SARS-CoV-2 RBD:ACE2 interaction has higher mechanical stability, larger binding free energy, and a lower dissociation rate compared to SARS-CoV-1, which helps to rationalize the different infection patterns of the two viruses. By studying how free ACE2 outcompetes tethered ACE2, we show that our assay is sensitive to prevention of bond formation by external binders. We expect our results to provide a way to investigate the roles of viral mutations and blocking agents for targeted pharmaceutical intervention.
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12
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Liu Z, Moreira RA, Dujmović A, Liu H, Yang B, Poma AB, Nash MA. Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex. NANO LETTERS 2022; 22:179-187. [PMID: 34918516 PMCID: PMC8759085 DOI: 10.1021/acs.nanolett.1c03584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/03/2021] [Indexed: 05/27/2023]
Abstract
We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from its target (CTLA-4), by pulling from eight different anchor residues. We found that pulling on the anticalin from residue 60 or 87 resulted in significantly higher rupture forces and a decrease in koff by 2-3 orders of magnitude over a force range of 50-200 pN. Five of the six internal anchor points gave rise to complexes significantly more stable than N- or C-terminal anchor points, rupturing at up to 250 pN at loading rates of 0.1-10 nN s-1. Anisotropic network modeling and molecular dynamics simulations helped to explain the geometric dependency of mechanostability. These results demonstrate that optimization of attachment residue position on therapeutic binding scaffolds can provide large improvements in binding strength, allowing for mechanical affinity maturation under shear stress without mutation of binding interface residues.
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Affiliation(s)
- Zhaowei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Rodrigo A. Moreira
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - Ana Dujmović
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Byeongseon Yang
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Adolfo B. Poma
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
- International
Center for Research on Innovative Biobased Materials (ICRI-BioM)—International
Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Michael A. Nash
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
- National
Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058 Basel, Switzerland
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13
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Wang Z, Nie J, Shi S, Li G, Zheng P. Transforming de novo protein α 3D into a mechanically stable protein by zinc binding. Chem Commun (Camb) 2021; 57:11489-11492. [PMID: 34651619 DOI: 10.1039/d1cc04908a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
α3D is a de novo designed three-helix bundle protein. Like most naturally occurring helical proteins, it is mechanically labile with an unfolding force of <15 pN, revealed by atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). This protein has been further designed with a tri-cysteine metal-binding site, named α3DIV, which can bind heavy transition metals. Here, we demonstrate that incorporating such a metal-binding site can transform this mechanically labile protein into a stable one. We show that zinc binds to the tri-cysteine site and increases the unfolding force to ∼160 pN. This force is one order of magnitude higher than that of the apo-protein (<15 pN). Moreover, the unfolding mechanism of Zn-α3DIV indicates the correct zinc binding with the tri-cysteine site, forming three mechanostable Zn-thiolate bonds. Thus, α3DIV could be a potential α-helical structure-based building block for synthesizing biomaterials with tunable mechanical properties.
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Affiliation(s)
- Ziyi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Shengcao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Guoqiang Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
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14
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Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
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15
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Zhang S, Wang L, Wu L, Li Z, Yang B, Hou Y, Lei L, Cheng S, He Q. Deciphering Single-Bacterium Adhesion Behavior Modulated by Extracellular Electron Transfer. NANO LETTERS 2021; 21:5105-5115. [PMID: 34086465 DOI: 10.1021/acs.nanolett.1c01062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
For bacterial adhesion and biofilm formation, a thorough understanding of the mechanism and effective modulating is lacking due to the complex extracellular electron transfer (EET) at bacteria-surface interfaces. Here, we explore the adhesion behavior of a model electroactive bacteria under various metabolic conditions by an integrated electrochemical single-cell force microscopy system. A nonlinear model between bacterial adhesion force and electric field intensity is established, which provides a theoretical foundation for precise tuning of bacterial adhesion strength by the surface potential and the direction and flux of electron flow. In particular, based on quantitative analyses with equivalent charge distribution modeling and wormlike chain numerical simulations, it is demonstrated that the chain conformation and unfolding events of outer membrane appendages are dominantly impacted by the dynamic bacterial EET processes. This reveals how the anisotropy of bacterial conductive structure can translate into the desired adhesion behavior in different scenarios.
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Affiliation(s)
- Shuomeng Zhang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Lei Wang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Liang Wu
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
| | - Zhongjian Li
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Institute of Zhejiang University, Quzhou, Quzhou 32400, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
| | - Bin Yang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Institute of Zhejiang University, Quzhou, Quzhou 32400, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
| | - Yang Hou
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Institute of Zhejiang University, Quzhou, Quzhou 32400, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
| | - Lecheng Lei
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Institute of Zhejiang University, Quzhou, Quzhou 32400, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
| | - Shaoan Cheng
- College of Energy Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Qinggang He
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Ningbo Research Institute, Zhejiang University, Ningbo, Zhejiang 315100, China
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16
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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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17
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Applications of atomic force microscopy in modern biology. Emerg Top Life Sci 2021; 5:103-111. [PMID: 33600596 DOI: 10.1042/etls20200255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/25/2020] [Accepted: 01/22/2021] [Indexed: 01/20/2023]
Abstract
Single-molecule force spectroscopy (SMFS) is an emerging tool to investigate mechanical properties of biomolecules and their responses to mechanical forces, and one of the most-used techniques for mechanical manipulation is the atomic force microscope (AFM). AFM was invented as an imaging tool which can be used to image biomolecules in sub-molecular resolution in physiological conditions. It can also be used as a molecular force probe for applying mechanical forces on biomolecules. In this brief review, we will provide exciting examples from recent literature which show how the advances in AFM have enabled us to gain deep insights into mechanical properties and mechanobiology of biomolecules. AFM has been applied to study mechanical properties of cells, tissues, microorganisms, viruses as well as biological macromolecules such as proteins. It has found applications in biomedical fields like cancer biology, where it has been used both in the diagnostic phases as well as drug discovery. AFM has been able to answer questions pertaining to mechanosensing by neurons, and mechanical changes in viruses during infection by the viral particles as well as the fundamental processes such as cell division. Fundamental questions related to protein folding have also been answered by SMFS like determination of energy landscape properties of variety of proteins and their correlation with their biological functions. A multipronged approach is needed to diversify the research, as a combination with optical spectroscopy and computer-based steered molecular dynamic simulations along with SMFS can help us gain further insights into the field of biophysics and modern biology.
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18
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Danielsen SPO, Beech HK, Wang S, El-Zaatari BM, Wang X, Sapir L, Ouchi T, Wang Z, Johnson PN, Hu Y, Lundberg DJ, Stoychev G, Craig SL, Johnson JA, Kalow JA, Olsen BD, Rubinstein M. Molecular Characterization of Polymer Networks. Chem Rev 2021; 121:5042-5092. [PMID: 33792299 DOI: 10.1021/acs.chemrev.0c01304] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polymer networks are complex systems consisting of molecular components. Whereas the properties of the individual components are typically well understood by most chemists, translating that chemical insight into polymer networks themselves is limited by the statistical and poorly defined nature of network structures. As a result, it is challenging, if not currently impossible, to extrapolate from the molecular behavior of components to the full range of performance and properties of the entire polymer network. Polymer networks therefore present an unrealized, important, and interdisciplinary opportunity to exert molecular-level, chemical control on material macroscopic properties. A barrier to sophisticated molecular approaches to polymer networks is that the techniques for characterizing the molecular structure of networks are often unfamiliar to many scientists. Here, we present a critical overview of the current characterization techniques available to understand the relation between the molecular properties and the resulting performance and behavior of polymer networks, in the absence of added fillers. We highlight the methods available to characterize the chemistry and molecular-level properties of individual polymer strands and junctions, the gelation process by which strands form networks, the structure of the resulting network, and the dynamics and mechanics of the final material. The purpose is not to serve as a detailed manual for conducting these measurements but rather to unify the underlying principles, point out remaining challenges, and provide a concise overview by which chemists can plan characterization strategies that suit their research objectives. Because polymer networks cannot often be sufficiently characterized with a single method, strategic combinations of multiple techniques are typically required for their molecular characterization.
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Affiliation(s)
- Scott P O Danielsen
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Haley K Beech
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shu Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Bassil M El-Zaatari
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Xiaodi Wang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | | | | | - Zi Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Patricia N Johnson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yixin Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David J Lundberg
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Georgi Stoychev
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Stephen L Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julia A Kalow
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael Rubinstein
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Departments of Biomedical Engineering and Physics, Duke University, Durham, North Carolina 27708, United States.,World Primer Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
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19
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Yang B, Liu H, Liu Z, Doenen R, Nash MA. Influence of Fluorination on Single-Molecule Unfolding and Rupture Pathways of a Mechanostable Protein Adhesion Complex. NANO LETTERS 2020; 20:8940-8950. [PMID: 33191756 PMCID: PMC7729889 DOI: 10.1021/acs.nanolett.0c04178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/08/2020] [Indexed: 05/25/2023]
Abstract
We investigated the influence of fluorination on unfolding and unbinding reaction pathways of a mechanostable protein complex comprising the tandem dyad XModule-Dockerin bound to Cohesin. Using single-molecule atomic force spectroscopy, we mapped the energy landscapes governing the unfolding and unbinding reactions. We then used sense codon suppression to substitute trifluoroleucine in place of canonical leucine globally in XMod-Doc. Although TFL substitution thermally destabilized XMod-Doc, it had little effect on XMod-Doc:Coh binding affinity at equilibrium. When we mechanically dissociated global TFL-substituted XMod-Doc from Coh, we observed the emergence of a new unbinding pathway with a lower energy barrier. Counterintuitively, when fluorination was restricted to Doc, we observed mechano-stabilization of the non-fluorinated neighboring XMod domain. This suggests that intramolecular deformation is modulated by fluorination and highlights the differences between equilibrium thermostability and non-equilibrium mechanostability. Future work is poised to investigate fluorination as a means to modulate mechanical properties of synthetic proteins and hydrogels.
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Affiliation(s)
- Byeongseon Yang
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Regina Doenen
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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20
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Melo MCR, Bernardi RC, de la Fuente-Nunez C, Luthey-Schulten Z. Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories. J Chem Phys 2020; 153:134104. [DOI: 10.1063/5.0018980] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Marcelo C. R. Melo
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Rafael C. Bernardi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Department of Physics, Auburn University, Auburn, Alabama 36849, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Zaida Luthey-Schulten
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
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21
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Liu Z, Liu H, Vera AM, Bernardi RC, Tinnefeld P, Nash MA. High force catch bond mechanism of bacterial adhesion in the human gut. Nat Commun 2020; 11:4321. [PMID: 32859904 PMCID: PMC7456326 DOI: 10.1038/s41467-020-18063-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022] Open
Abstract
Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble substrates under hydrodynamic flow. Here we report the molecular mechanism behind an ultrastable protein complex responsible for resisting shear forces and adhering bacteria to cellulose fibers in the human gut. Using single-molecule force spectroscopy (SMFS), single-molecule FRET (smFRET), and molecular dynamics (MD) simulations, we resolve two binding modes and three unbinding reaction pathways of a mechanically ultrastable R. champanellensis (Rc) Dockerin:Cohesin (Doc:Coh) complex. The complex assembles in two discrete binding modes with significantly different mechanical properties, with one breaking at ~500 pN and the other at ~200 pN at loading rates from 1-100 nN s-1. A neighboring X-module domain allosterically regulates the binding interaction and inhibits one of the low-force pathways at high loading rates, giving rise to a catch bonding mechanism that manifests under force ramp protocols. Multi-state Monte Carlo simulations show strong agreement with experimental results, validating the proposed kinetic scheme. These results explain mechanistically how gut microbes regulate cell adhesion strength at high shear stress through intricate molecular mechanisms including dual-binding modes, mechanical allostery and catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
- Department of Physics, Auburn University, 36849, Auburn, AL, USA
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
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22
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Li Y, Cheng J, Delparastan P, Wang H, Sigg SJ, DeFrates KG, Cao Y, Messersmith PB. Molecular design principles of Lysine-DOPA wet adhesion. Nat Commun 2020; 11:3895. [PMID: 32753588 PMCID: PMC7403305 DOI: 10.1038/s41467-020-17597-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
The mussel byssus has long been a source of inspiration for the adhesion community. Recently, adhesive synergy between flanking lysine (Lys, K) and 3,4-Dihydroxyphenylalanine (DOPA, Y) residues in the mussel foot proteins (Mfps) has been highlighted. However, the complex topological relationship of DOPA and Lys as well as the interfacial adhesive roles of other amino acids have been understudied. Herein, we study adhesion of Lys and DOPA-containing peptides to organic and inorganic substrates using single-molecule force spectroscopy (SMFS). We show that a modest increase in peptide length, from KY to (KY)3, increases adhesion strength to TiO2. Surprisingly, further increase in peptide length offers no additional benefit. Additionally, comparison of adhesion of dipeptides containing Lys and either DOPA (KY) or phenylalanine (KF) shows that DOPA is stronger and more versatile. We furthermore demonstrate that incorporating a nonadhesive spacer between (KY) repeats can mimic the hidden length in the Mfp and act as an effective strategy to dissipate energy.
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Affiliation(s)
- Yiran Li
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
- Department of Physics, Nanjing University, 210093, Nanjing, P. R. China
| | - Jing Cheng
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
| | - Peyman Delparastan
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
| | - Haoqi Wang
- Department of Physics, Nanjing University, 210093, Nanjing, P. R. China
| | - Severin J Sigg
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
| | - Kelsey G DeFrates
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
| | - Yi Cao
- Department of Physics, Nanjing University, 210093, Nanjing, P. R. China
| | - Phillip B Messersmith
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA.
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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23
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Galera-Prat A, Vera AM, Moraïs S, Vazana Y, Bayer EA, Carrión-Vázquez M. Impact of scaffoldin mechanostability on cellulosomal activity. Biomater Sci 2020; 8:3601-3610. [PMID: 32232253 DOI: 10.1039/c9bm02052g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignocellulose is the most abundant renewable carbon source in the biosphere. However, the main bottleneck in its conversion to produce second generation biofuels is the saccharification step: the hydrolysis of lignocellulosic material into soluble fermentable sugars. Some anaerobic bacteria have developed an extracellular multi-enzyme complex called the cellulosome that efficiently degrades cellulosic substrates. Cellulosome complexes rely on enzyme-integrating scaffoldins that are large non-catalytic scaffolding proteins comprising several cohesin modules and additional functional modules that mediate the anchoring of the complex to the cell surface and the specific binding to its cellulosic substrate. It was proposed that mechanical forces may affect the cohesins positioned between the cell- and cellulose-anchoring points in the so-called connecting region. Consequently, the mechanical resistance of cohesins within the scaffoldin is of great importance, both to understand cellulosome function and as a parameter of industrial interest, to better mimic natural complexes through the use of the established designer cellulosome technology. Here we study how the mechanical stability of cohesins in a scaffoldin affects the enzymatic activity of a cellulosome. We found that when a cohesin of low mechanical stability is positioned in the connecting region of a scaffoldin, the activity of the resulting cellulosome is reduced as opposed to a cohesin of higher mechanical stability. This observation directly relates mechanical stability of the scaffoldin-borne cohesins to cellulosome activity and provides a rationale for the design of artificial cellulosomes for industrial applications, by incorporating mechanical stability as a new industrial parameter in the biotechnology toolbox.
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Affiliation(s)
- Albert Galera-Prat
- Instituto Cajal, Department of Molecular, Cellular and Developmental Neurobiology. IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain.
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24
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Yang B, Liu Z, Liu H, Nash MA. Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes. Front Mol Biosci 2020; 7:85. [PMID: 32509800 PMCID: PMC7248566 DOI: 10.3389/fmolb.2020.00085] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.
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Affiliation(s)
- Byeongseon Yang
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhaowei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Haipei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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25
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Bao Y, Luo Z, Cui S. Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials. Chem Soc Rev 2020; 49:2799-2827. [PMID: 32236171 DOI: 10.1039/c9cs00855a] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.
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Affiliation(s)
- Yu Bao
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China.
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26
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Sedlak SM, Schendel LC, Gaub HE, Bernardi RC. Streptavidin/biotin: Tethering geometry defines unbinding mechanics. SCIENCE ADVANCES 2020; 6:eaay5999. [PMID: 32232150 PMCID: PMC7096159 DOI: 10.1126/sciadv.aay5999] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/03/2020] [Indexed: 05/26/2023]
Abstract
Macromolecules tend to respond to applied forces in many different ways. Chemistry at high shear forces can be intriguing, with relatively soft bonds becoming very stiff in specific force-loading geometries. Largely used in bionanotechnology, an important case is the streptavidin (SA)/biotin interaction. Although SA's four subunits have the same affinity, we find that the forces required to break the SA/biotin bond depend strongly on the attachment geometry. With AFM-based single-molecule force spectroscopy (SMFS), we measured unbinding forces of biotin from different SA subunits to range from 100 to more than 400 pN. Using a wide-sampling approach, we carried out hundreds of all-atom steered molecular dynamics (SMD) simulations for the entire system, including molecular linkers. Our strategy revealed the molecular mechanism that causes a fourfold difference in mechanical stability: Certain force-loading geometries induce conformational changes in SA's binding pocket lowering the energy barrier, which biotin has to overcome to escape the pocket.
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Affiliation(s)
- Steffen M. Sedlak
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany
| | - Leonard C. Schendel
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany
| | - Hermann E. Gaub
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany
| | - Rafael C. Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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27
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Extreme mechanical stability in protein complexes. Curr Opin Struct Biol 2020; 60:124-130. [DOI: 10.1016/j.sbi.2019.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/14/2019] [Accepted: 11/27/2019] [Indexed: 12/21/2022]
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28
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Ma X, Zhu M, Liu J, Li X, Qu L, Liang L, Huang W, Wang J, Li N, Chen JH, Zhang W, Yu Z. Interactions between PHD3-Bromo of MLL1 and H3K4me3 Revealed by Single-Molecule Magnetic Tweezers in a Parallel DNA Circuit. Bioconjug Chem 2019; 30:2998-3006. [PMID: 31714753 DOI: 10.1021/acs.bioconjchem.9b00665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-molecule force spectroscopy is a powerful tool to directly measure protein-protein interactions (PPI). The high specificity and precision of PPI measurements made it possible to reveal detailed mechanisms of intermolecular interactions. However, protein aggregation due to specific or nonspecific interactions is among the most challenging problems in PPI examination. Here, we propose a strategy of a parallel DNA circuit to probe PPI using single-molecule magnetic tweezers. In contrast to PPI examination using atomic force microscopy, microspheres as probes used in magnetic tweezers avoided the single-probe issue of a cantilever. Negatively charged DNA as a linker circumvented the severe aggregation in the PPI construct with a protein linker. The unnatural amino acid encoded in proteins of interest expanded the choices of biorthogonal conjugation. We demonstrated how to apply our strategy to probe the PPI between the PHD3-Bromo and the histone H3 methylated at K4, a critical epigenetic event in leukemia development. We found a rupture force of 12 pN for breaking the PPI, which is much higher than that required to peel DNA off from a nucleosome, 3 pN. We expect that our methods will make PPI measurements of mechanics and kinetics with great precision, facilitating PPI-related research, e.g., PPI-targeted drug discovery.
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Affiliation(s)
- Xiaofeng Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Manning Zhu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Jianyu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , China
| | - Xu Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Lihua Qu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Junli Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Ning Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases , Key Laboratory of Parasite and Vector Biology, Ministry of Health , Shanghai 200025 , China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy , Nankai University , 38 Tongyan Rd , Tianjin 300353 , China
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29
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Bernardi RC, Durner E, Schoeler C, Malinowska KH, Carvalho BG, Bayer EA, Luthey-Schulten Z, Gaub HE, Nash MA. Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. J Am Chem Soc 2019; 141:14752-14763. [PMID: 31464132 PMCID: PMC6939381 DOI: 10.1021/jacs.9b06776] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Can molecular dynamics
simulations predict the mechanical behavior of protein complexes?
Can simulations decipher the role of protein domains of unknown function
in large macromolecular complexes? Here, we employ a wide-sampling
computational approach to demonstrate that molecular dynamics simulations,
when carefully performed and combined with single-molecule atomic
force spectroscopy experiments, can predict and explain the behavior
of highly mechanostable protein complexes. As a test case, we studied
a previously unreported homologue from Ruminococcus flavefaciens called X-module-Dockerin (XDoc) bound to its partner Cohesin (Coh).
By performing dozens of short simulation replicas near the rupture
event, and analyzing dynamic network fluctuations, we were able to
generate large simulation statistics and directly compare them with
experiments to uncover the mechanisms involved in mechanical stabilization.
Our single-molecule force spectroscopy experiments show that the XDoc-Coh
homologue complex withstands forces up to 1 nN at loading rates of
105 pN/s. Our simulation results reveal that this remarkable
mechanical stability is achieved by a protein architecture that directs
molecular deformation along paths that run perpendicular to the pulling
axis. The X-module was found to play a crucial role in shielding the
adjacent protein complex from mechanical rupture. These mechanisms
of protein mechanical stabilization have potential applications in
biotechnology for the development of systems exhibiting shear enhanced
adhesion or tunable mechanics.
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Affiliation(s)
- Rafael C Bernardi
- Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ellis Durner
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Constantin Schoeler
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Klara H Malinowska
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Bruna G Carvalho
- School of Chemical Engineering , University of Campinas , 13083-852 Campinas , Brazil
| | - Edward A Bayer
- Department of Biomolecular Sciences , Weizmann Institute of Science , 76100 Rehovot , Israel
| | - Zaida Luthey-Schulten
- Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , 80799 Munich , Germany
| | - Michael A Nash
- Department of Chemistry , University of Basel , 4058 Basel , Switzerland.,Department of Biosystems Science and Engineering , ETH Zurich , 4058 Basel , Switzerland
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30
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Broken force dispersal network in tip-links by the mutations at the Ca 2+-binding residues induces hearing-loss. Biochem J 2019; 476:2411-2425. [PMID: 31399498 PMCID: PMC6717114 DOI: 10.1042/bcj20190453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022]
Abstract
Tip-link as force-sensor in hearing conveys the mechanical force originating from sound to ion-channels while maintaining the integrity of the entire sensory assembly in the inner ear. This delicate balance between structure and function of tip-links is regulated by Ca2+-ions present in endolymph. Mutations at the Ca2+-binding sites of tip-links often lead to congenital deafness, sometimes syndromic defects impairing vision along with hearing. Although such mutations are already identified, it is still not clear how the mutants alter the structure-function properties of the force-sensors associated with diseases. With an aim to decipher the differences in force-conveying properties of the force-sensors in molecular details, we identified the conformational variability of mutant and wild-type tip-links at the single-molecule level using FRET at the endolymphatic Ca2+ concentrations and subsequently measured the force-responsive behavior using single-molecule force spectroscopy with an Atomic Force Microscope (AFM). AFM allowed us to mimic the high and wide range of force ramps (103-106 pN s-1) as experienced in the inner ear. We performed in silico network analysis to learn that alterations in the conformations of the mutants interrupt the natural force-propagation paths through the sensors and make the mutant tip-links vulnerable to input forces from sound stimuli. We also demonstrated that a Ca2+ rich environment can restore the force-response of the mutant tip-links which may eventually facilitate the designing of better therapeutic strategies to the hearing loss.
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31
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Liu H, Schittny V, Nash MA. Removal of a Conserved Disulfide Bond Does Not Compromise Mechanical Stability of a VHH Antibody Complex. NANO LETTERS 2019; 19:5524-5529. [PMID: 31257893 PMCID: PMC6975629 DOI: 10.1021/acs.nanolett.9b02062] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/28/2019] [Indexed: 05/28/2023]
Abstract
Single-domain VHH antibodies are promising reagents for medical therapy. A conserved disulfide bond within the VHH framework region is known to be critical for thermal stability, however, no prior studies have investigated its influence on the stability of VHH antibody-antigen complexes under mechanical load. Here, we used single-molecule force spectroscopy to test the influence of a VHH domain's conserved disulfide bond on the mechanical strength of the interaction with its antigen mCherry. We found that although removal of the disulfide bond through cysteine-to-alanine mutagenesis significantly lowered VHH domain denaturation temperature, it had no significant impact on the mechanical strength of the VHH:mCherry interaction with complex rupture occurring at ∼60 pN at 103-104 pN/sec regardless of disulfide bond state. These results demonstrate that mechanostable binding interactions can be built on molecular scaffolds that may be thermodynamically compromised at equilibrium.
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Affiliation(s)
- Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Valentin Schittny
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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32
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Yuan G, Ma Q, Wu T, Wang M, Li X, Zuo J, Zheng P. Multistep Protein Unfolding Scenarios from the Rupture of a Complex Metal Cluster Cd 3S 9. Sci Rep 2019; 9:10518. [PMID: 31324867 PMCID: PMC6642161 DOI: 10.1038/s41598-019-47004-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
Protein (un)folding is a complex and essential process. With the rapid development of single-molecule techniques, we can detect multiple and transient proteins (un)folding pathways/intermediates. However, the observation of multiple multistep (>2) unfolding scenarios for a single protein domain remains limited. Here, we chose metalloprotein with relatively stable and multiple metal-ligand coordination bonds as a system for such a purpose. Using AFM-based single-molecule force spectroscopy (SMFS), we successfully demonstrated the complex and multistep protein unfolding scenarios of the β-domain of a human protein metallothionein-3 (MT). MT is a protein of ~60 amino acids (aa) in length with 20 cysteines for various metal binding, and the β-domain (βMT) is of ~30 aa with an M3S9 metal cluster. We detected four different types of three-step protein unfolding scenarios from the Cd-βMT, which can be possibly explained by the rupture of Cd-S bonds in the complex Cd3S9 metal cluster. In addition, complex unfolding scenarios with four rupture peaks were observed. The Cd-S bonds ruptured in both single bond and multiple bonds modes. Our results provide not only evidence for multistep protein unfolding phenomena but also reveal unique properties of metalloprotein system using single-molecule AFM.
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Affiliation(s)
- Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Qun Ma
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Mengdi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Jinglin Zuo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China.
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33
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Sedlak SM, Schendel LC, Melo MCR, Pippig DA, Luthey-Schulten Z, Gaub HE, Bernardi RC. Direction Matters: Monovalent Streptavidin/Biotin Complex under Load. NANO LETTERS 2019; 19:3415-3421. [PMID: 30346175 PMCID: PMC6486461 DOI: 10.1021/acs.nanolett.8b04045] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Novel site-specific attachment strategies combined with improvements of computational resources enable new insights into the mechanics of the monovalent biotin/streptavidin complex under load and forced us to rethink the diversity of rupture forces reported in the literature. We discovered that the mechanical stability of this complex depends strongly on the geometry in which force is applied. By atomic force microscopy-based single molecule force spectroscopy we found unbinding of biotin to occur beyond 400 pN at force loading rates of 10 nN/s when monovalent streptavidin was tethered at its C-terminus. This value is about twice as high than that for N-terminal attachment. Steered molecular dynamics simulations provided a detailed picture of the mechanics of the unbinding process in the corresponding force loading geometries. Using machine learning techniques, we connected findings from hundreds of simulations to the experimental results, identifying different force propagation pathways. Interestingly, we observed that depending on force loading geometry, partial unfolding of N-terminal region of monovalent streptavidin occurs before biotin is released from the binding pocket.
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Affiliation(s)
- Steffen M. Sedlak
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany
| | - Leonard C. Schendel
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany
| | - Marcelo C. R. Melo
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Diana A. Pippig
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany
| | - Zaida Luthey-Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hermann E. Gaub
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany
| | - Rafael C. Bernardi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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34
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Milles LF, Unterauer EM, Nicolaus T, Gaub HE. Calcium stabilizes the strongest protein fold. Nat Commun 2018; 9:4764. [PMID: 30420680 PMCID: PMC6232131 DOI: 10.1038/s41467-018-07145-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022] Open
Abstract
Staphylococcal pathogens adhere to their human targets with exceptional resilience to mechanical stress, some propagating force to the bacterium via small, Ig-like folds called B domains. We examine the mechanical stability of these folds using atomic force microscopy-based single-molecule force spectroscopy. The force required to unfold a single B domain is larger than 2 nN – the highest mechanostability of a protein to date by a large margin. B domains coordinate three calcium ions, which we identify as crucial for their extreme mechanical strength. When calcium is removed through chelation, unfolding forces drop by a factor of four. Through systematic mutations in the calcium coordination sites we can tune the unfolding forces from over 2 nN to 0.15 nN, and dissect the contribution of each ion to B domain mechanostability. Their extraordinary strength, rapid refolding and calcium-tunable force response make B domains interesting protein design targets. Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.
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Affiliation(s)
- Lukas F Milles
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany.
| | - Eduard M Unterauer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany
| | - Thomas Nicolaus
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany.
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35
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Haataja TJK, Bernardi RC, Lecointe S, Capoulade R, Merot J, Pentikäinen U. Non-syndromic Mitral Valve Dysplasia Mutation Changes the Force Resilience and Interaction of Human Filamin A. Structure 2018; 27:102-112.e4. [PMID: 30344108 DOI: 10.1016/j.str.2018.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/24/2018] [Accepted: 09/18/2018] [Indexed: 01/03/2023]
Abstract
Filamin A (FLNa), expressed in endocardial endothelia during fetal valve morphogenesis, is key in cardiac development. Missense mutations in FLNa cause non-syndromic mitral valve dysplasia (FLNA-MVD). Here, we aimed to reveal the currently unknown underlying molecular mechanism behind FLNA-MVD caused by the FLNa P637Q mutation. The solved crystal structure of the FLNa3-5 P637Q revealed that this mutation causes only minor structural changes close to mutation site. These changes were observed to significantly affect FLNa's ability to transmit cellular force and to interact with its binding partner. The performed steered molecular dynamics simulations showed that significantly lower forces are needed to split domains 4 and 5 in FLNA-MVD than with wild-type FLNa. The P637Q mutation was also observed to interfere with FLNa's interactions with the protein tyrosine phosphatase PTPN12. Our results provide a crucial step toward understanding the molecular bases behind FLNA-MVD, which is critical for the development of drug-based therapeutics.
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Affiliation(s)
- Tatu J K Haataja
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Rafael C Bernardi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Simon Lecointe
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | | | - Jean Merot
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Ulla Pentikäinen
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, 40014 Jyväskylä, Finland; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute of Biomedicine, University of Turku, 20520 Turku, Finland; Turku Centre for Biotechnology, University of Turku, 20520 Turku, Finland.
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36
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Verdorfer T, Gaub HE. Ligand Binding Stabilizes Cellulosomal Cohesins as Revealed by AFM-based Single-Molecule Force Spectroscopy. Sci Rep 2018; 8:9634. [PMID: 29941985 PMCID: PMC6018229 DOI: 10.1038/s41598-018-27085-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022] Open
Abstract
The cohesin-dockerin receptor-ligand family is the key element in the formation of multi-enzyme lignocellulose-digesting extracellular complexes called cellulosomes. Changes in a receptor protein upon binding of a ligand - commonly referred to as allostery - are not just essential for signalling, but may also alter the overall mechanical stability of a protein receptor. Here, we measured the change in mechanical stability of a library of cohesin receptor domains upon binding of their dockerin ligands in a multiplexed atomic force microscopy-based single-molecule force spectroscopy experiment. A parallelized, cell-free protein expression and immobilization protocol enables rapid mechanical phenotyping of an entire library of constructs with a single cantilever and thus ensures high throughput and precision. Our results show that dockerin binding increases the mechanical stability of every probed cohesin independently of its original folding strength. Furthermore, our results indicate that certain cohesins undergo a transition from a multitude of different folds or unfolding pathways to a single stable fold upon binding their ligand.
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Affiliation(s)
- Tobias Verdorfer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799, Munich, Germany.
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799, Munich, Germany
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37
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Milles LF, Schulten K, Gaub HE, Bernardi RC. Molecular mechanism of extreme mechanostability in a pathogen adhesin. Science 2018; 359:1527-1533. [PMID: 29599244 DOI: 10.1126/science.aar2094] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/01/2018] [Indexed: 01/08/2023]
Abstract
High resilience to mechanical stress is key when pathogens adhere to their target and initiate infection. Using atomic force microscopy-based single-molecule force spectroscopy, we explored the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β. Steered molecular dynamics simulations revealed, and single-molecule force spectroscopy experiments confirmed, the mechanism by which this complex withstands forces of over 2 nanonewtons, a regime previously associated with the strength of a covalent bond. The target peptide, confined in a screwlike manner in the binding pocket of SdrG, distributes forces mainly toward the peptide backbone through an intricate hydrogen bond network. Thus, these adhesins can attach to their target with exceptionally resilient mechanostability, virtually independent of peptide side chains.
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Affiliation(s)
- Lukas F Milles
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstrasse 54, 80799 Munich, Germany
| | - Klaus Schulten
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstrasse 54, 80799 Munich, Germany.
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Sumbul F, Marchesi A, Rico F. History, rare, and multiple events of mechanical unfolding of repeat proteins. J Chem Phys 2018; 148:123335. [PMID: 29604819 DOI: 10.1063/1.5013259] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.
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Affiliation(s)
- Fidan Sumbul
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
| | - Arin Marchesi
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
| | - Felix Rico
- U1006, Aix-Marseille Université and INSERM, 163 Avenue de Luminy, 13009 Marseille, France
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