1
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Gomes DEB, Yang B, Vanella R, Nash MA, Bernardi RC. Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. J Am Chem Soc 2024; 146:23842-23853. [PMID: 39146039 DOI: 10.1021/jacs.4c05869] [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: 08/17/2024]
Abstract
Understanding binding epitopes involved in protein-protein interactions and accurately determining their structure are long-standing goals with broad applicability in industry and biomedicine. Although various experimental methods for binding epitope determination exist, these approaches are typically low throughput and cost-intensive. Computational methods have potential to accelerate epitope predictions; however, recently developed artificial intelligence (AI)-based methods frequently fail to predict epitopes of synthetic binding domains with few natural homologues. Here we have developed an integrated method employing generalized-correlation-based dynamic network analysis on multiple molecular dynamics (MD) trajectories, initiated from AlphaFold2Multimer structures, to unravel the structure and binding epitope of the therapeutic PD-L1:Affibody complex. Both AlphaFold2 and conventional molecular dynamics trajectory analysis were ineffective in distinguishing between two proposed binding models, parallel and perpendicular. However, our integrated approach, utilizing dynamic network analysis, demonstrated that the perpendicular mode was significantly more stable. These predictions were validated using a suite of experimental epitope mapping protocols, including cross-linking mass spectrometry and next-generation sequencing-based deep mutational scanning. Conversely, AlphaFold3 failed to predict a structure bound in the perpendicular pose, highlighting the necessity for exploratory research in the search for binding epitopes and challenging the notion that AI-generated protein structures can be accepted without scrutiny. Our research underscores the potential of employing dynamic network analysis to enhance AI-based structure predictions for more accurate identification of protein-protein interaction interfaces.
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Affiliation(s)
- Diego E B Gomes
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Byeongseon Yang
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel 4058, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Rafael C Bernardi
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
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2
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Xu Q, Zhao Z, Chen X, Fan W, Jiang Y. The Impact of Surface Modifier on Magnetic Nanoparticle Properties and Their Application in CD3+T Cell Separation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39024471 DOI: 10.1021/acs.langmuir.4c01332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Fe3O4 nanoparticles occupy a pivotal position in the realm of nanobiology due to their nontoxic, biocompatible, and superparamagnetic properties. This study examines the influence of surface modifiers on the properties of magnetic nanoparticles. Poly(methacrylic acid) (PMAA), poly(4-styrenesulfonic acid-co-maleic acid) sodium salt (PSSM), trisodium citrate (TSC), carboxymethylcellulose (CMC), and carboxymethylated-dextran 40 (CMD40) were introduced into a one-pot solvothermal method to synthesize magnetic nanoparticles. TEM, the 4-(bromomethyl)-6,7-dimethoxy coumarin (BMMC) absorption assay, and the Bradford method were employed to characterize the diameter, carboxyl content, and protein immobilization ability of the nanoparticles, respectively. The findings revealed that CMD40-modified magnetic nanoparticles (CMD40-MNPs) exhibited the highest carboxyl content and streptavidin (SA) immobilization content, reaching 6.5 × 10-7 mol/mg and 375 μg/mg, respectively. In contrast, CMC-modified magnetic nanoparticles displayed opposite trends. This is primarily attributed to dextran's unique molecular structure, which enhances its water solubility and biocompatibility, thereby facilitating contact with Fe3O4 nanoparticles in aqueous solutions. CMD40-MNPs possess a saturation magnetization value of 60.90 emu/g and can be collected within (60 ± 5) s using a standard magnetic separator. Cytotoxicity assays demonstrated that CMD40-MNPs are nontoxic to cells. A cell sorting strategy utilizing the binding of SA-CMD40-MNPs and biotin antihuman CD3 antibody-modified cell suspensions was employed to isolate CD3+T cells. The results indicate that the purity and efficiency of targeted CD3+T cells are 85.2% and 61.5%, respectively.
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Affiliation(s)
- Qianrui Xu
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Zhimin Zhao
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Xinyu Chen
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Wenqian Fan
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yong Jiang
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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3
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Fernandez‐Calvo A, Reifs A, Saa L, Cortajarena AL, De Sancho D, Perez‐Jimenez R. The strongest protein binder is surprisingly labile. Protein Sci 2024; 33:e5030. [PMID: 38864696 PMCID: PMC11168069 DOI: 10.1002/pro.5030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
Bacterial adhesins are cell-surface proteins that anchor to the cell wall of the host. The first stage of infection involves the specific attachment to fibrinogen (Fg), a protein found in human blood. This attachment allows bacteria to colonize tissues causing diseases such as endocarditis. The study of this family of proteins is hence essential to develop new strategies to fight bacterial infections. In the case of the Gram-positive bacterium Staphylococcus aureus, there exists a class of adhesins known as microbial surface components recognizing adhesive matrix molecules (MSCRAMMs). Here, we focus on one of them, the clumping factor A (ClfA), which has been found to bind Fg through the dock-lock-latch mechanism. Interestingly, it has recently been discovered that MSCRAMM proteins employ a catch-bond to withstand forces exceeding 2 nN, making this type of interaction as mechanically strong as a covalent bond. However, it is not known whether this strength is an evolved feature characteristic of the bacterial protein or is typical only of the interaction with its partner. Here, we combine single-molecule force spectroscopy, biophysical binding assays, and molecular simulations to study the intrinsic mechanical strength of ClfA. We find that despite the extremely high forces required to break its interactions with Fg, ClfA is not by itself particularly strong. Integrating the results from both theory and experiments we dissect contributions to the mechanical stability of this protein.
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Affiliation(s)
- Alba Fernandez‐Calvo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA)DerioBizkaiaSpain
| | - Antonio Reifs
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA)DerioBizkaiaSpain
| | - Laura Saa
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
| | - Aitziber L. Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA)Donostia‐San SebastiánSpain
- Ikerbasque Foundation for ScienceBilbaoSpain
| | - David De Sancho
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, University of the Basque Country (UPV/EHU)San SebastianSpain
- Donostia International Physics Center (DIPC)San SebastianSpain
| | - Raul Perez‐Jimenez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA)DerioBizkaiaSpain
- Ikerbasque Foundation for ScienceBilbaoSpain
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4
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Yang B, Gomes DEB, Liu Z, Santos MS, Li J, Bernardi RC, Nash MA. Engineering the Mechanical Stability of a Therapeutic Affibody/PD-L1 Complex by Anchor Point Selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595133. [PMID: 38826272 PMCID: PMC11142103 DOI: 10.1101/2024.05.21.595133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Protein-protein complexes can vary in mechanical stability depending on the direction from which force is applied. Here we investigated the anisotropic mechanical stability of a molecular complex between a therapeutic non-immunoglobulin scaffold called Affibody and the extracellular domain of the immune checkpoint protein PD-L1. We used a combination of single-molecule AFM force spectroscopy (AFM-SMFS) with bioorthogonal clickable peptide handles, shear stress bead adhesion assays, molecular modeling, and steered molecular dynamics (SMD) simulations to understand the pulling point dependency of mechanostability of the Affibody:(PD-L1) complex. We observed diverse mechanical responses depending on the anchor point. For example, pulling from residue #22 on Affibody generated an intermediate unfolding event attributed to partial unfolding of PD-L1, while pulling from Affibody's N-terminus generated force-activated catch bond behavior. We found that pulling from residue #22 or #47 on Affibody generated the highest rupture forces, with the complex breaking at up to ~ 190 pN under loading rates of ~104-105 pN/sec, representing a ~4-fold increase in mechanostability as compared with low force N-terminal pulling. SMD simulations provided consistent tendencies in rupture forces, and through visualization of force propagation networks provided mechanistic insights. These results demonstrate how mechanostability of therapeutic protein-protein interfaces can be controlled by informed selection of anchor points within molecules, with implications for optimal bioconjugation strategies in drug delivery vehicles.
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Affiliation(s)
- Byeongseon Yang
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Diego E. B. Gomes
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Zhaowei Liu
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
- Present address: Department of Bionanoscience, Delft University of Technology, 2629HZ Delft, the Netherlands
| | - Mariana Sá Santos
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Jiajun Li
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Rafael C. Bernardi
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Michael A. Nash
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
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5
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Lu Y, Wen J, Wang C, Wang M, Jiang F, Miao L, Xu M, Li Y, Chen X, Chen Y. Mesophilic Argonaute-Based Single Polystyrene Sphere Aptamer Fluorescence Platform for the Multiplexed and Ultrasensitive Detection of Non-Nucleic Acid Targets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308424. [PMID: 38081800 DOI: 10.1002/smll.202308424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Indexed: 01/04/2024]
Abstract
The rapid, simultaneous, and accurate identification of multiple non-nucleic acid targets in clinical or food samples at room temperature is essential for public health. Argonautes (Agos) are guided, programmable, target-activated, next-generation nucleic acid endonucleases that could realize one-pot and multiplexed detection using a single enzyme, which cannot be achieved with CRISPR/Cas. However, currently reported thermophilic Ago-based multi-detection sensors are mainly employed in the detection of nucleic acids. Herein, this work proposes a Mesophilic Argonaute Report-based single millimeter Polystyrene Sphere (MARPS) multiplex detection platform for the simultaneous analysis of non-nucleic acid targets. The aptamer is utilized as the recognition element, and a single millimeter-sized polystyrene sphere (PSmm) with a large concentration of guide DNA on the surface served as the microreactor. These are combined with precise Clostridium butyricum Ago (CbAgo) cleavage and exonuclease I (Exo I) signal amplification to achieve the efficient and sensitive recognition of non-nucleic acid targets, such as mycotoxins (<60 pg mL-1) and pathogenic bacteria (<102 cfu mL-1). The novel MARPS platform is the first to use mesophilic Agos for the multiplex detection of non-nucleic acid targets, overcoming the limitations of CRISPR/Cas in this regard and representing a major advancement in non-nucleic acid target detection using a gene-editing-based system.
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Affiliation(s)
- Yingying Lu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junping Wen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chengming Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mengjiao Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Feng Jiang
- Laboratory of Detection Technology of Focus Chemical Hazards in Animal-derived Food for State Market Regulation, Hubei Provincial Institute for Food Supervision and Test, Wuhan, 430075, China
| | - Lin Miao
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Minggao Xu
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaohua Chen
- Department of Laboratory Medicine, General Hospital of Central Theater Command, Wuhan, 430070, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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6
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Liu Z, Liu H, Vera AM, Yang B, Tinnefeld P, Nash MA. Engineering an artificial catch bond using mechanical anisotropy. Nat Commun 2024; 15:3019. [PMID: 38589360 PMCID: PMC11001878 DOI: 10.1038/s41467-024-46858-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Catch bonds are a rare class of protein-protein interactions where the bond lifetime increases under an external pulling force. Here, we report how modification of anchor geometry generates catch bonding behavior for the mechanostable Dockerin G:Cohesin E (DocG:CohE) adhesion complex found on human gut bacteria. Using AFM single-molecule force spectroscopy in combination with bioorthogonal click chemistry, we mechanically dissociate the complex using five precisely controlled anchor geometries. When tension is applied between residue #13 on CohE and the N-terminus of DocG, the complex behaves as a two-state catch bond, while in all other tested pulling geometries, including the native configuration, it behaves as a slip bond. We use a kinetic Monte Carlo model with experimentally derived parameters to simulate rupture force and lifetime distributions, achieving strong agreement with experiments. Single-molecule FRET measurements further demonstrate that the complex does not exhibit dual binding mode behavior at equilibrium but unbinds along multiple pathways under force. Together, these results show how mechanical anisotropy and anchor point selection can be used to engineer artificial catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Department of Bionanoscience, Delft University of Technology, 2629HZ, Delft, the Netherlands
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Byeongseon Yang
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland.
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
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7
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Zuo J, Chen H, Li H. Two molecule force spectroscopy on ligand-receptor interactions. NANOSCALE 2023; 15:16581-16589. [PMID: 37740375 DOI: 10.1039/d3nr03428c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Many biological processes involve the rupture of multiple ligand-receptors or multivalent ligand-receptors. It is challenging to study the rupture of such parallelly arranged multiple ligand-receptors due to the difficulties in engineering such systems in a well-controlled fashion. Here we report the use of two-molecule force spectroscopy to investigate the rupture of two parallelly arranged monomeric streptavidin (mSA)-biotin complexes. By using SpyCatcher-SpyTag chemistry, we successfully engineered a molecular twin of biotin, in which two biotins are arranged in parallel. By reacting mSA with twin biotin, we constructed parallelly arranged two mSA-biotin complexes for force spectroscopy experiments. The incorporation of single molecule fingerprint domains into our mSA-biotin dimers allowed us to identify and assign the rupture events of the parallelly arranged mSA-biotin complexes without any ambiguity in the two-molecule force spectroscopy experiments. Our results revealed that the rupture force of the parallel dimer mSA-biotin is 172 pN at a pulling speed of 400 nm s-1, which is about 1.6 times of that of single mSA-biotin (105 pN). Furthermore, our findings indicate that the two mSA-biotin behave as non-interacting, independent ligand-receptors. The strategy we demonstrated here can be extended to other ligand-receptors and may open up an avenue toward rigorously testing the theoretic predictions proposed in various models regarding the rupture of multiple parallel ligand-receptors.
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Affiliation(s)
- Jiacheng Zuo
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - Hui Chen
- Department of Chemical Engineering, Nanjing Forestry University, Nanjing, Jiangsu, P. R. China
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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8
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Hao H, Cai H, Yang B, Lou S, Guo Z, Lu W, Tian Z. Versatile DNA Balances via Adjacent Base Stacking for Homogeneous Assay of Energy Parameters, Small Molecules, And Ribonuclease. Anal Chem 2023; 95:14643-14650. [PMID: 37733486 DOI: 10.1021/acs.analchem.3c02431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Homogeneous assays often obviate any separation and washing steps, thus minimizing the risks of contamination and false positive. DNA toehold exchange is a homogeneous, reversible process whose thermodynamic properties can be finely tuned for various assay applications. However, the developed probes often rely on direct interactions of analytes with DNA strands involved in toehold exchange, limiting the versatility of probe design. Here, the coaxial adjacent stacking between one auxiliary strand and another invading strand offers a favorable ΔG to shift one DNA balance, while the auxiliary strand is independent of the DNA balance itself. Therefore, such a DNA balance allowed fine tuning of the equilibrium via adjustment of the auxiliary strand alone. The energy contribution of base stacking can be quantified in a homogeneous solution based on the difference in the equilibrium constant. Besides, the proof of concept for DNA balance allows effective assay of a small molecule or ribonuclease in a homogeneous solution. This novel DNA balance via adjacent base stacking provides an interesting alternative to homogeneously assay various analytes.
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Affiliation(s)
- Huimin Hao
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Hanfen Cai
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Bin Yang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Shuyan Lou
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Zihua Guo
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Weiyi Lu
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
| | - Zhen Tian
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 410005, P. R. China
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9
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Melo MCR, Bernardi RC. Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike. Biophys J 2023; 122:2833-2840. [PMID: 36738105 PMCID: PMC10398237 DOI: 10.1016/j.bpj.2023.01.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Over a century ago, physicists started broadly relying on theoretical models to guide new experiments. Soon thereafter, chemists began doing the same. Now, biological research enters a new era when experiment and theory walk hand in hand. Novel software and specialized hardware became essential to understand experimental data and propose new models. In fact, current petascale computing resources already allow researchers to reach unprecedented levels of simulation throughput to connect in silico and in vitro experiments. The reduction in cost and improved access allowed a large number of research groups to adopt supercomputing resources and techniques. Here, we outline how large-scale computing has evolved to expand decades-old research, spark new research efforts, and continuously connect simulation and observation. For instance, multiple publicly and privately funded groups have dedicated extensive resources to develop artificial intelligence tools for computational biophysics, from accelerating quantum chemistry calculations to proposing protein structure models. Moreover, advances in computer hardware have accelerated data processing from single-molecule experimental observations and simulations of chemical reactions occurring throughout entire cells. The combination of software and hardware has opened the way for exascale computing and the production of the first public exascale supercomputer, Frontier, inaugurated by the Oak Ridge National Laboratory in 2022. Ultimately, the popularization and development of computational techniques and the training of researchers to use them will only accelerate the diversification of tools and learning resources for future generations.
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Affiliation(s)
- Marcelo C R Melo
- Auburn University, Department of Physics, Auburn University, Auburn, Alabama
| | - Rafael C Bernardi
- Auburn University, Department of Physics, Auburn University, Auburn, Alabama.
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10
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Cai W, Jäger M, Bullerjahn JT, Hugel T, Wolf S, Balzer BN. Anisotropic Friction in a Ligand-Protein Complex. NANO LETTERS 2023; 23:4111-4119. [PMID: 36948207 DOI: 10.1021/acs.nanolett.2c04632] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The effect of an externally applied directional force on molecular friction is so far poorly understood. Here, we study the force-driven dissociation of the ligand-protein complex biotin-streptavidin and identify anisotropic friction as a not yet described type of molecular friction. Using AFM-based stereographic single molecule force spectroscopy and targeted molecular dynamics simulations, we find that the rupture force and friction for biotin-streptavidin vary with the pulling angle. This observation holds true for friction extracted from Kramers' rate expression and by dissipation-corrected targeted molecular dynamics simulations based on Jarzynski's identity. We rule out ligand solvation and protein-internal friction as sources of the angle-dependent friction. Instead, we observe a heterogeneity in free energy barriers along an experimentally uncontrolled orientation parameter, which increases the rupture force variance and therefore the overall friction. We anticipate that anisotropic friction needs to be accounted for in a complete understanding of friction in biomolecular dynamics and anisotropic mechanical environments.
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Affiliation(s)
- Wanhao Cai
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Miriam Jäger
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
| | - Jakob T Bullerjahn
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Hermann-Herder-Str. 3, 79104 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
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11
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Iida S, Kameda T. Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation. J Chem Inf Model 2023. [PMID: 37188657 DOI: 10.1021/acs.jcim.2c01529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Steered molecular dynamics (SMD) simulations are used to study molecular dissociation events by applying a harmonic force to the molecules and pulling them at a constant velocity. Instead of constant-velocity pulling, we use a constant force: the constant-force SMD (CF-SMD) simulation. The CF-SMD simulation employs a constant force to reduce the activation barrier of molecular dissociation, thereby enhancing the dissociation event. Here, we present the capability of the CF-SMD simulation to estimate the dissociation time at equilibrium. We performed all-atom CF-SMD simulations for NaCl and protein-ligand systems, producing dissociation time at various forces. We extrapolated these values to the dissociation rate without a constant force using Bell's model or the Dudko-Hummer-Szabo model. We demonstrate that the CF-SMD simulations with the models predicted the dissociation time in equilibrium. A CF-SMD simulation is a powerful tool for estimating the dissociation rate in a direct and computationally efficient manner.
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Affiliation(s)
- Shinji Iida
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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12
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Obeng EM, Steer DL, Fulcher AJ, Wagstaff KM. Sortase A transpeptidation produces seamless, unbranched biotinylated nanobodies for multivalent and multifunctional applications. NANOSCALE ADVANCES 2023; 5:2251-2260. [PMID: 37056610 PMCID: PMC10089078 DOI: 10.1039/d3na00014a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Exploitation of the biotin-streptavidin interaction for advanced protein engineering is used in many bio-nanotechnology applications. As such, researchers have used diverse techniques involving chemical and enzyme reactions to conjugate biotin to biomolecules of interest for subsequent docking onto streptavidin-associated molecules. Unfortunately, the biotin-streptavidin interaction is susceptible to steric hindrance and conformational malformation, leading to random orientations that ultimately impair the function of the displayed biomolecule. To minimize steric conflicts, we employ sortase A transpeptidation to produce quantitative, seamless, and unbranched nanobody-biotin conjugates for efficient display on streptavidin-associated nanoparticles. We further characterize the protein-nanoparticle complex and demonstrate its usefulness in optical microscopy and multivalent severe acute respiratory syndrome coronavirus (SARS-CoV-2) antigen interaction. The approach reported here provides a template for making novel multivalent and multifunctional protein complexes for avidity-inspired technologies.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
| | - David L Steer
- Monash Proteomics and Metabolomics Facility, Monash University Clayton VIC 3800 Australia
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University Clayton VIC 3800 Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University Clayton VIC 3800 Australia
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13
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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: 2] [Impact Index Per Article: 2.0] [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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14
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Melo MCR, Gomes DEB, Bernardi RC. Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections. J Am Chem Soc 2023; 145:70-77. [PMID: 36455202 DOI: 10.1021/jacs.2c07674] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The unbinding pathway of a protein complex can vary significantly depending on biochemical and mechanical factors. Under mechanical stress, a complex may dissociate through a mechanism different from that used in simple thermal dissociation, leading to different dissociation rates under shear force and thermal dissociation. This is a well-known phenomenon studied in biomechanics whose molecular and atomic details are still elusive. A particularly interesting case is the complex formed by bacterial adhesins with their human peptide target. These protein interactions have a force resilience equivalent to those of covalent bonds, an order of magnitude stronger than the widely used streptavidin:biotin complex, while having an ordinary affinity, much lower than that of streptavidin:biotin. Here, in an in silico single-molecule force spectroscopy approach, we use molecular dynamics simulations to investigate the dissociation mechanism of adhesin/peptide complexes. We show how the Staphylococcus epidermidis adhesin SdrG uses a catch-bond mechanism to increase complex stability with increasing mechanical stress. While allowing for thermal dissociation in a low-force regime, an entirely different mechanical dissociation path emerges in a high-force regime, revealing an intricate mechanism that does not depend on the peptide's amino acid sequence. Using a dynamic network analysis approach, we identified key amino acid contacts that describe the mechanics of this complex, revealing differences in dynamics that hinder thermal dissociation and establish the mechanical dissociation path. We then validate the information content of the selected amino acid contacts using their dynamics to successfully predict the rupture forces for this complex through a machine learning model.
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Affiliation(s)
- Marcelo C R Melo
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Diego E B Gomes
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Rafael C Bernardi
- Department of Physics, Auburn University, Auburn, Alabama 36849, United States
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15
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Paiva T, Viljoen A, da Costa TM, Geoghegan JA, Dufrêne YF. Interaction of the Staphylococcus aureus Surface Protein FnBPB with Corneodesmosin Involves Two Distinct, Extremely Strong Bonds. ACS NANOSCIENCE AU 2022; 3:58-66. [PMID: 36820093 PMCID: PMC9936583 DOI: 10.1021/acsnanoscienceau.2c00036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 02/17/2023]
Abstract
Attachment of Staphylococcus aureus to human skin corneocyte cells plays a critical role in exacerbating the severity of atopic dermatitis (AD). Pathogen-skin adhesion is mediated by bacterial cell-surface proteins called adhesins, including fibronectin-binding protein B (FnBPB). FnBPB binds to corneodesmosin (CDSN), a glycoprotein exposed on AD patient corneocytes. Using single-molecule experiments, we demonstrate that CDSN binding by FnBPB relies on a sophisticated two-site mechanism. Both sites form extremely strong bonds with binding forces of ∼1 and ∼2.5 nN albeit with faster dissociation rates than those reported for homologues of the adhesin. This previously unidentified two-binding site interaction in FnBPB illustrates its remarkable variety of adhesive functions and is of biological significance as the high strength and short bond lifetime will favor efficient skin colonization by the pathogen.
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Affiliation(s)
- Telmo
O. Paiva
- Louvain
Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Albertus Viljoen
- Louvain
Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Thaina M. da Costa
- Department
of Microbiology, Moyne Institute of Preventive Medicine, School of
Genetics and Microbiology, Trinity College
Dublin, Dublin 2, Ireland
| | - Joan A. Geoghegan
- Department
of Microbiology, Moyne Institute of Preventive Medicine, School of
Genetics and Microbiology, Trinity College
Dublin, Dublin 2, Ireland,Institute
of Microbiology and Infection, University
of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.,
| | - Yves F. Dufrêne
- Louvain
Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, L7.07.07, B-1348 Louvain-la-Neuve, Belgium,
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16
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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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17
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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: 10] [Impact Index Per Article: 5.0] [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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18
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Lei H, Zhang J, Li Y, Wang X, Qin M, Wang W, Cao Y. Histidine-Specific Bioconjugation for Single-Molecule Force Spectroscopy. ACS NANO 2022; 16:15440-15449. [PMID: 35980082 DOI: 10.1021/acsnano.2c07298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Atomic force microscopy (AFM) based single-molecule force spectroscopy (SMFS) is a powerful tool to study the mechanical properties of proteins. In these experiments, site-specific immobilization of proteins is critical, as the tether determines the direction and amplitude of forces applied to the protein of interest. However, existing methods are mainly based on thiol chemistry or specific protein tags, which cannot meet the need of many challenging experiments. Here, we developed a histidine-specific phosphorylation strategy to covalently anchor proteins to an AFM cantilever tip or the substrate via their histidine tag or surface-exposed histidine residues. The formed covalent linkage was mechanically stable with rupture forces of over 1.3 nN. This protein immobilization method considerably improved the pickup rate and data quality of SMFS experiments. We further demonstrated the use of this method to explore the pulling-direction-dependent mechanical stability of green fluorescent protein and the unfolding of the membrane protein archaerhodopsin-3.
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Affiliation(s)
- Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 163 Xianlin Road, Nanjing 210023, People's Republic of China
| | - Junsheng Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Ying Li
- Institute of Advanced Materials and Flexible Electronics (IAMFE), School of Chemistry and Materials Science, Nanjing University of Information Science & Technology 219 Ningliu Road, Nanjing, 210044, People's Republic of China
| | - Xin Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 163 Xianlin Road, Nanjing 210023, People's Republic of China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, People's Republic of China
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19
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Maciuba K, Kaiser CM. Tethering Complex Proteins and Protein Complexes for Optical Tweezers Experiments. Methods Mol Biol 2022; 2478:427-460. [PMID: 36063330 PMCID: PMC9924098 DOI: 10.1007/978-1-0716-2229-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tethering proteins to force probes, typically micrometer-sized beads, is a prerequisite for dissecting their properties with optical tweezers. DNA handles serve as spacers between the tethered protein of interest and the bead surface. Attachment sites of the DNA handles to both the surface of beads and to the protein of interest must be mechanically stable for optical tweezers experiments. The most prominent method for attaching DNA handles to proteins utilizes thiol chemistry, linking modified DNA to engineered cysteines in the target protein. This method, although experimentally straightforward, is impractical for the large number of proteins that endogenously contain multiple or essential cysteines at undesired positions. Here, we describe two alternative approaches that take advantage of genetically encoded tag sequences in the target protein. The first method uses the enzymes Sfp and BirA, and the second uses the more recently described SpyTag-SpyCatcher system. We outline the process of generating the DNA handles themselves, as well as how to make the DNA-protein chimeras for carrying out optical tweezers experiments. These methods have robustly worked for several diverse and complex proteins, including ones that are difficult to produce or purify, and for protein-containing complexes such as the ribosome. They will be useful in cases where chemistry-based approaches are impractical or not feasible.
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Affiliation(s)
- Kevin Maciuba
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Christian M Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
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20
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Huang W, Le S, Sun Y, Lin DJ, Yao M, Shi Y, Yan J. Mechanical Stabilization of a Bacterial Adhesion Complex. J Am Chem Soc 2022; 144:16808-16818. [PMID: 36070862 PMCID: PMC9501914 DOI: 10.1021/jacs.2c03961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The adhesions between Gram-positive bacteria and their
hosts are
exposed to varying magnitudes of tensile forces. Here, using an ultrastable
magnetic tweezer-based single-molecule approach, we show the catch-bond
kinetics of the prototypical adhesion complex of SD-repeat protein
G (SdrG) to a peptide from fibrinogen β (Fgβ) over a physiologically
important force range from piconewton (pN) to tens of pN, which was
not technologically accessible to previous studies. At 37 °C,
the lifetime of the complex exponentially increases from seconds at
several pN to ∼1000 s as the force reaches 30 pN, leading to
mechanical stabilization of the adhesion. The dissociation transition
pathway is determined as the unbinding of a critical β-strand
peptide (“latch” strand of SdrG that secures the entire
adhesion complex) away from its binding cleft, leading to the dissociation
of the Fgβ ligand. Similar mechanical stabilization behavior
is also observed in several homologous adhesions, suggesting the generality
of catch-bond kinetics in such bacterial adhesions. We reason that
such mechanical stabilization confers multiple advantages in the pathogenesis
and adaptation of bacteria.
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Affiliation(s)
- Wenmao Huang
- Department of Physics, National University of Singapore, Singapore 117542.,Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Shimin Le
- Department of Physics, National University of Singapore, Singapore 117542.,Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Yuze Sun
- Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Dennis Jingxiong Lin
- Department of Physics, National University of Singapore, Singapore 117542.,Mechanobiology Institute, National University of Singapore, Singapore 117411
| | - Mingxi Yao
- Mechanobiology Institute, National University of Singapore, Singapore 117411.,Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi Shi
- Institute of Materials Research and Engineering, A*STAR, 2 Fusionopolis Way, Innovis, #08-03, Singapore 138634
| | - Jie Yan
- Department of Physics, National University of Singapore, Singapore 117542.,Mechanobiology Institute, National University of Singapore, Singapore 117411.,Centre for Bioimaging Sciences, National University of Singapore, Singapore 117546
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21
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Kim JM, Kang YM. Optical Fluorescence Imaging of Native Proteins Using a Fluorescent Probe with a Cell-Membrane-Permeable Carboxyl Group. Int J Mol Sci 2022; 23:ijms23105841. [PMID: 35628651 PMCID: PMC9143923 DOI: 10.3390/ijms23105841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/07/2022] [Accepted: 05/21/2022] [Indexed: 12/10/2022] Open
Abstract
Although various methods for selective protein tagging have been established, their ap plications are limited by the low fluorescent tagging efficiency of specific terminal regions of the native proteins of interest (NPIs). In this study, the highly sensitive fluorescence imaging of single NPIs was demonstrated using a eukaryotic translation mechanism involving a free carboxyl group of a cell-permeable fluorescent dye. In living cells, the carboxyl group of cell-permeable fluorescent dyes reacted with the lysine residues of acceptor peptides (AP or AVI-Tag). Genetically encoded recognition demonstrated that the efficiency of fluorescence labeling was nearly 100%. Nickel-nitrilotriacetic acid (Ni-NTA) beads bound efficiently to a single NPI for detection in a cell without purification. Our labeling approach satisfied the necessary conditions for measuring fluorescently labeled NPI using universal carboxyl fluorescent dyes. This approach is expected to be useful for resolving complex biological/ecological issues and robust single-molecule analyses of dynamic processes, in addition to applications in ultra-sensitive NPIs detection using nanotechnology.
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Affiliation(s)
- Jung Min Kim
- BK21 FOUR R&E Center for Environmental Science and Ecological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02842, Korea
- Correspondence: ; Tel.: +82-2-3290-4778
| | - Young-Mi Kang
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea;
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22
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Santos MS, Liu H, Schittny V, Vanella R, Nash MA. Correlating single-molecule rupture mechanics with cell population adhesion by yeast display. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 35284851 PMCID: PMC8904261 DOI: 10.1016/j.bpr.2021.100035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022]
Affiliation(s)
- Mariana Sá Santos
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Systems Biology PhD program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Haipei Liu
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Valentin Schittny
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Rosario Vanella
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Michael A. Nash
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Corresponding author
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23
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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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24
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Nie J, Tian F, Zheng B, Wang Z, Zheng P. Exploration of Metal-Ligand Coordination Bonds in Proteins by Single-molecule Force Spectroscopy. CHEM LETT 2021. [DOI: 10.1246/cl.210307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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25
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Konyshev I, Byvalov A. Model systems for optical trapping: the physical basis and biological applications. Biophys Rev 2021; 13:515-529. [PMID: 34471436 DOI: 10.1007/s12551-021-00823-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/05/2021] [Indexed: 11/30/2022] Open
Abstract
The micromechanical methods, among which optical trapping and atomic force microscopy have a special place, are widespread currently in biology to study molecular interactions between different biological objects. Optical trapping is reported to be quite applicable to study the mechanical properties of surface structures onto bacterial (pili and flagella) and eukaryotic (filopodia) cells. The review briefly summarizes the physical basis of optical trapping, as well as the principles of calculating the van der Waals, electrostatic, and donor-acceptor forces when two microparticles or a microparticle and a flat surface are used. Three main types of model systems (abiotic, biotic, and mixed) used in trapping experiments are described, and the peculiarities of manipulation with living (bacteria, fungal spores, etc.) and non-spherical objects (e.g., rod-shaped bacteria) are summarized.
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Affiliation(s)
- Ilya Konyshev
- Institute of Physiology of Коmi Science Centre of the Ural Branch of the Russian Academy of Sciences, FRC Komi SC UB RAS, Komi Republic, 167982 Syktyvkar, Russian Federation.,Vyatka State University, 36 Moskovskaya str, 610000 Kirov, Russian Federation
| | - Andrey Byvalov
- Institute of Physiology of Коmi Science Centre of the Ural Branch of the Russian Academy of Sciences, FRC Komi SC UB RAS, Komi Republic, 167982 Syktyvkar, Russian Federation.,Vyatka State University, 36 Moskovskaya str, 610000 Kirov, Russian Federation
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26
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Berger RML, Weck JM, Kempe SM, Hill O, Liedl T, Rädler JO, Monzel C, Heuer-Jungemann A. Nanoscale FasL Organization on DNA Origami to Decipher Apoptosis Signal Activation in Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101678. [PMID: 34057291 DOI: 10.1002/smll.202101678] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Indexed: 05/27/2023]
Abstract
Cell signaling is initiated by characteristic protein patterns in the plasma membrane, but tools to decipher their molecular organization and activation are hitherto lacking. Among the well-known signaling pattern is the death inducing signaling complex with a predicted hexagonal receptor architecture. To probe this architecture, DNA origami-based nanoagents with nanometer precise arrangements of the death receptor ligand FasL are introduced and presented to cells. Mimicking different receptor geometries, these nanoagents act as signaling platforms inducing fastest time-to-death kinetics for hexagonal FasL arrangements with 10 nm inter-molecular spacing. Compared to naturally occurring soluble FasL, this trigger is faster and 100× more efficient. Nanoagents with different spacing, lower FasL number or higher coupling flexibility impede signaling. The results present DNA origami as versatile signaling scaffolds exhibiting unprecedented control over molecular number and geometry. They define molecular benchmarks in apoptosis signal initiation and constitute a new strategy to drive particular cell responses.
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Affiliation(s)
- Ricarda M L Berger
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Johann M Weck
- Max Planck Institute of Biochemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-University, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Simon M Kempe
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Oliver Hill
- Apogenix AG, University of Heidelberg, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Heinrich-Heine University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-University, Am Klopferspitz 18, 82152, Martinsried, Germany
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27
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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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28
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Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D. Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chem Rev 2020; 121:11701-11725. [PMID: 33166471 DOI: 10.1021/acs.chemrev.0c00617] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.
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Affiliation(s)
- Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Hermann E Gaub
- Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 München, Germany
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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29
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Gruber S, Löf A, Sedlak SM, Benoit M, Gaub HE, Lipfert J. Designed anchoring geometries determine lifetimes of biotin-streptavidin bonds under constant load and enable ultra-stable coupling. NANOSCALE 2020; 12:21131-21137. [PMID: 33079117 DOI: 10.1039/d0nr03665j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The small molecule biotin and the homotetrameric protein streptavidin (SA) form a stable and robust complex that plays a pivotal role in many biotechnological and medical applications. In particular, the SA-biotin linkage is frequently used in single-molecule force spectroscopy (SMFS) experiments. Recent data suggest that SA-biotin bonds show strong directional dependence and a broad range of multi-exponential lifetimes under load. Here, we investigate engineered SA variants with different valencies and a unique tethering point under constant forces using a magnetic tweezers assay. We observed orders-of-magnitude differences in the lifetimes under force, which we attribute to the distinct force-loading geometries in the different SA variants. Lifetimes showed exponential dependencies on force, with extrapolated lifetimes at zero force that are similar for the different SA variants and agree with parameters determined from constant-speed dynamic SMFS experiments. We identified an especially long-lived tethering geometry that will facilitate ultra-stable SMFS experiments.
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Affiliation(s)
- Sophia Gruber
- Department of Physics and Center for NanoScience, LMU Munich, Germany.
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30
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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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31
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Lecot S, Chevolot Y, Phaner-Goutorbe M, Yeromonahos C. Impact of Silane Monolayers on the Adsorption of Streptavidin on Silica and Its Subsequent Interactions with Biotin: Molecular Dynamics and Steered Molecular Dynamics Simulations. J Phys Chem B 2020; 124:6786-6796. [PMID: 32663028 DOI: 10.1021/acs.jpcb.0c04382] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein adsorption on surfaces is used in analytical tools as an immobilization mean to trap the analyte to be detected. However, protein adsorption can lead to a conformational change in the protein structure, resulting in a loss of bioactivity. Here, we study adsorption of a streptavidin-biotin complex on amorphous SiO2 surfaces functionalized with five different silane self-assembled monolayers by all-atom molecular dynamics simulations. We find that the streptavidin global conformational change, as well as the nature of residues with high mobility, depends on the alkyl chain length and head-group charge of silane molecules. Effects on interactions with biotin are further investigated by steered molecular dynamics (SMD) simulations, which mimics atomic force microscopy (AFM) with the biotin attached on the tip. We show the combined effects of adsorption-induced global conformational changes and of the position of residues with high mobility on the streptavidin-biotin rupture force. By comparing our results to experimental and SMD rupture forces obtained in water, without any surface, we conclude that silane with uncharged and short alkyl chains allows streptavidin immobilization, while keeping biotin interactions better than silanes with long alkyl chains or charged head groups.
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Affiliation(s)
- Solène Lecot
- Université de Lyon, Institut des Nanotechnologies de Lyon UMR 5270, Ecole Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
| | - Yann Chevolot
- Université de Lyon, Institut des Nanotechnologies de Lyon UMR 5270, Ecole Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
| | - Magali Phaner-Goutorbe
- Université de Lyon, Institut des Nanotechnologies de Lyon UMR 5270, Ecole Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
| | - Christelle Yeromonahos
- Université de Lyon, Institut des Nanotechnologies de Lyon UMR 5270, Ecole Centrale de Lyon, 36 avenue Guy de Collongue, 69134 Ecully, France
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32
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Mathelié-Guinlet M, Chantraine C, Viela F, Pietrocola G, Speziale P, Dufrêne YF. Nanomechanics of the molecular complex between staphylococcal adhesin SpsD and elastin. NANOSCALE 2020; 12:13996-14003. [PMID: 32578656 DOI: 10.1039/d0nr02745f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Staphylococcus pseudintermedius surface protein SpsD binds to extracellular matrix proteins to invade canine epithelial cells. Using single-molecule experiments, we show that SpsD engages in two modes of interaction with elastin that are tightly controlled by physical stress. Binding is weak (∼100 pN) at low tensile force (i.e. loading rate), but is dramatically enhanced (up to ∼1500 pN) by mechanical tension. Consistent with a "dock, lock, and latch" (DLL) mechanism, this force represents among the highest mechanical strengths known for a non-covalent biological interaction. The transition from weak to strong binding correlates with an increase in molecular stiffness but, surprisingly, with a decrease in molecular extension. This unanticipated mechanical behavior indicates that the adhesin is engaged in two distinct interaction mechanisms. Our results emphasize the crucial role of protein nanomechanics in the adhesion of staphylococci, and illustrate their wide diversity of force-dependent ligand-binding activities. These single-molecule mechanical experiments may contribute to the development of antiadhesion approaches to treat infections caused by S. pseudintermedius and other bacterial pathogens engaged in DLL interactions.
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Affiliation(s)
- Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium.
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33
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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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34
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Schendel LC, Bauer MS, Sedlak SM, Gaub HE. Single-Molecule Manipulation in Zero-Mode Waveguides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906740. [PMID: 32141169 DOI: 10.1002/smll.201906740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/08/2020] [Indexed: 06/10/2023]
Abstract
The mechanobiology of receptor-ligand interactions and force-induced enzymatic turnover can be revealed by simultaneous measurements of force response and fluorescence. Investigations at physiologically relevant high labeled substrate concentrations require total internal reflection fluorescence microscopy or zero mode waveguides (ZMWs), which are difficult to combine with atomic force microscopy (AFM). A fully automatized workflow is established to manipulate single molecules inside ZMWs autonomously with noninvasive cantilever tip localization. A protein model system comprising a receptor-ligand pair of streptavidin blocked with a biotin-tagged ligand is introduced. The ligand is pulled out of streptavidin by an AFM cantilever leaving the receptor vacant for reoccupation by freely diffusing fluorescently labeled biotin, which can be detected in single-molecule fluorescence concurrently to study rebinding rates. This work illustrates the potential of the seamless fusion of these two powerful single-molecule techniques.
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Affiliation(s)
- Leonard C Schendel
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Amalienstrasse 54, Munich, 80799, Germany
| | - Magnus S Bauer
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Amalienstrasse 54, Munich, 80799, Germany
| | - Steffen M Sedlak
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Amalienstrasse 54, Munich, 80799, Germany
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Amalienstrasse 54, Munich, 80799, Germany
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35
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Abstract
The complex of the small molecule biotin and the homotetrameric protein streptavidin is key to a broad range of biotechnological applications. Therefore, the behavior of this extraordinarily high-affinity interaction under mechanical force is intensively studied by single-molecule force spectroscopy. Recently, steered molecular dynamics simulations have identified a low force pathway for the dissociation of biotin from streptavidin, which involves partial unfolding of the N-terminal β-sheet structure of monovalent streptavidin's functional subunit. Based on these results, we now introduced two mutations (T18C,A33C) in the functional subunit of monovalent streptavidin to establish a switchable connection (disulfide bridge) between the first two β-strands to prevent this unfolding. In atomic force microscopy-based single-molecule force spectroscopy experiments, we observed unbinding forces of about 350 pN (at a force-loading rate of 10 nN s-1) for pulling a single biotin out of an N-terminally anchored monovalent streptavidin binding pocket - about 1.5-fold higher compared with what has been reported for N-terminal force loading of native monovalent streptavidin. Upon addition of a reducing agent, the unbinding forces dropped back to 200 pN, as the disulfide bridge was destroyed. Switching from reducing to oxidizing buffer conditions, the inverse effect was observed. Our work illustrates how the mechanics of a receptor-ligand system can be tuned by engineering the receptor protein far off the ligand-binding pocket.
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Affiliation(s)
- Leonard C Schendel
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 Munich, Germany.
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36
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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: 57] [Impact Index Per Article: 14.3] [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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37
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Dahal N, Nowitzke J, Eis A, Popa I. Binding-Induced Stabilization Measured on the Same Molecular Protein Substrate Using Single-Molecule Magnetic Tweezers and Heterocovalent Attachments. J Phys Chem B 2020; 124:3283-3290. [DOI: 10.1021/acs.jpcb.0c00167] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
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38
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Kluger C, Braun L, Sedlak SM, Pippig DA, Bauer MS, Miller K, Milles LF, Gaub HE, Vogel V. Different Vinculin Binding Sites Use the Same Mechanism to Regulate Directional Force Transduction. Biophys J 2020; 118:1344-1356. [PMID: 32109366 PMCID: PMC7091509 DOI: 10.1016/j.bpj.2019.12.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/17/2019] [Accepted: 12/30/2019] [Indexed: 12/18/2022] Open
Abstract
Vinculin is a universal adaptor protein that transiently reinforces the mechanical stability of adhesion complexes. It stabilizes mechanical connections that cells establish between the actomyosin cytoskeleton and the extracellular matrix via integrins or to neighboring cells via cadherins, yet little is known regarding its mechanical design. Vinculin binding sites (VBSs) from different nonhomologous actin-binding proteins use conserved helical motifs to associate with the vinculin head domain. We studied the mechanical stability of such complexes by pulling VBS peptides derived from talin, α-actinin, and Shigella IpaA out of the vinculin head domain. Experimental data from atomic force microscopy single-molecule force spectroscopy and steered molecular dynamics (SMD) simulations both revealed greater mechanical stability of the complex for shear-like than for zipper-like pulling configurations. This suggests that reinforcement occurs along preferential force directions, thus stabilizing those cytoskeletal filament architectures that result in shear-like pulling geometries. Large force-induced conformational changes in the vinculin head domain, as well as protein-specific fine-tuning of the VBS sequence, including sequence inversion, allow for an even more nuanced force response.
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Affiliation(s)
- Carleen Kluger
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lukas Braun
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Steffen M Sedlak
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Diana A Pippig
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Magnus S Bauer
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ken Miller
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lukas F Milles
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Viola Vogel
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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39
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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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40
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Franz F, Daday C, Gräter F. Advances in molecular simulations of protein mechanical properties and function. Curr Opin Struct Biol 2020; 61:132-138. [PMID: 31954324 DOI: 10.1016/j.sbi.2019.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 01/05/2023]
Abstract
Single-molecule force spectroscopy and classical molecular dynamics are natural allies. Recent advances in both experiments and simulations have increasingly facilitated a direct comparison of SMFS and MD data, most importantly by closing the gap between time scales, which has been traditionally at least 5 orders of magnitudes wide. In this review, we will explore these advances chiefly on the computational side. We focus on protein dynamics under force and highlight recent studies that showcase how lower loading rates and more statistics help to better interpret previous experiments and to also motivate new ones. At the same time, steadily increasing system sizes are used to mimic more closely the mechanical environment in the biological context. We showcase some of these advances on atomistic and coarse-grained scale, from asymmetric membrane tension to larger (multidomain/multimeric) protein assemblies under force.
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Affiliation(s)
- Florian Franz
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, 69120 Heidelberg, Germany
| | - Csaba Daday
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Frauke Gräter
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, 69120 Heidelberg, Germany.
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41
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Mathews R, Ramya L. A comparative study for the intermediate states of myelin oligodendrocyte glycoprotein in the absence and presence of glycan - A computational approach. J Mol Graph Model 2019; 96:107517. [PMID: 31881468 DOI: 10.1016/j.jmgm.2019.107517] [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: 11/15/2019] [Revised: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 10/25/2022]
Abstract
Myelin Oligodendrocyte glycoprotein (MOG) is found to play an important role in providing structural integrity to myelin sheath at the same time it acts as an auto-antigen which might lead to Multiple Sclerosis (MS). What causes this specific property of being an auto-antigen is still not known. Here we present molecular dynamics simulation studies of unfolding and folding of the protein MOG in both the absence and presence of N-glycan in order to understand the role of glycosylation in the stability and flexibility of the protein. The main results from these studies show that the glycosylation increases the stability of the protein MOG and inhibits the complete unfolding of MOG in the SMD. From the folding studies using TMD, it was observed that the glycan helps the protein to attain the near-native folded conformation. However, it was also observed from the direct TMD studies that the pathway of protein folding was enhanced by the trace-back of intermediate states in the presence of glycan.
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Affiliation(s)
- Rita Mathews
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamilnadu, India
| | - L Ramya
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamilnadu, India.
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42
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Li Y, Cao Y. The molecular mechanisms underlying mussel adhesion. NANOSCALE ADVANCES 2019; 1:4246-4257. [PMID: 36134404 PMCID: PMC9418609 DOI: 10.1039/c9na00582j] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 10/09/2019] [Indexed: 06/12/2023]
Abstract
Marine mussels are able to firmly affix on various wet surfaces by the overproduction of special mussel foot proteins (mfps). Abundant fundamental studies have been conducted to understand the molecular basis of mussel adhesion, where the catecholic amino acid, l-3,4-dihydroxyphenylalanine (DOPA) has been found to play the major role. These studies continue to inspire the engineering of novel adhesives and coatings with improved underwater performances. Despite the fact that the recent advances of adhesives and coatings inspired by mussel adhesive proteins have been intensively reviewed in literature, the fundamental biochemical and biophysical studies on the origin of the strong and versatile wet adhesion have not been fully covered. In this review, we show how the force measurements at the molecular level by surface force apparatus (SFA) and single molecule atomic force microscopy (AFM) can be used to reveal the direct link between DOPA and the wet adhesion strength of mussel proteins. We highlight a few important technical details that are critical to the successful experimental design. We also summarize many new insights going beyond DOPA adhesion, such as the surface environment and protein sequence dependent synergistic and cooperative binding. We also provide a perspective on a few uncharted but outstanding questions for future studies. A comprehensive understanding on mussel adhesion will be beneficial to the design of novel synthetic wet adhesives for various biomedical applications.
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Affiliation(s)
- Yiran Li
- Shenzhen Research Institute of Nanjing University Shenzhen 518057 China
- Department of Physics, Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Soli State Microstructure, Nanjing University Nanjing 210093 China
| | - Yi Cao
- Shenzhen Research Institute of Nanjing University Shenzhen 518057 China
- Department of Physics, Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Soli State Microstructure, Nanjing University Nanjing 210093 China
- Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210093 China
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43
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Li Y, Xu Y, Kurths J, Duan J. The influences of correlated spatially random perturbations on first passage time in a linear-cubic potential. CHAOS (WOODBURY, N.Y.) 2019; 29:101102. [PMID: 31675827 DOI: 10.1063/1.5116626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
The influences of correlated spatially random perturbations (SRPs) on the first passage problem are studied in a linear-cubic potential with a time-changing external force driven by a Gaussian white noise. First, the escape rate in the absence of SRPs is obtained by Kramers' theory. For the random potential case, we simplify the escape rate by multiplying the escape rate of smooth potentials with a specific coefficient, which is to evaluate the influences of randomness. Based on this assumption, the escape rates are derived in two scenarios, i.e., small/large correlation lengths. Consequently, the first passage time distributions (FPTDs) are generated for both smooth and random potential cases. We find that the position of the maximal FPTD has a very good agreement with that of numerical results, which verifies the validity of the proposed approximations. Besides, with increasing the correlation length, the FPTD shifts to the left gradually and tends to the smooth potential case. Second, we investigate the most probable passage time (MPPT) and mean first passage time (MFPT), which decrease with increasing the correlation length. We also find that the variation ranges of both MPPT and MFPT increase nonlinearly with increasing the intensity. Besides, we briefly give constraint conditions to guarantee the validity of our approximations. This work enables us to approximately evaluate the influences of the correlation length of SRPs in detail, which was always ignored previously.
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Affiliation(s)
- Yongge Li
- Center for Mathematical Sciences & School of Mathematics and Statistics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yong Xu
- Department of Applied Mathematics, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jürgen Kurths
- Center for Mathematical Sciences & School of Mathematics and Statistics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinqiao Duan
- Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois 60616, USA
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Multiplexed protein force spectroscopy reveals equilibrium protein folding dynamics and the low-force response of von Willebrand factor. Proc Natl Acad Sci U S A 2019; 116:18798-18807. [PMID: 31462494 PMCID: PMC6754583 DOI: 10.1073/pnas.1901794116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule force spectroscopy has provided unprecedented insights into protein folding, force regulation, and function. So far, the field has relied primarily on atomic force microscope and optical tweezers assays that, while powerful, are limited in force resolution, throughput, and require feedback for constant force measurements. Here, we present a modular approach based on magnetic tweezers (MT) for highly multiplexed protein force spectroscopy. Our approach uses elastin-like polypeptide linkers for the specific attachment of proteins, requiring only short peptide tags on the protein of interest. The assay extends protein force spectroscopy into the low force (<1 pN) regime and enables parallel and ultra-stable measurements at constant forces. We present unfolding and refolding data for the small, single-domain protein ddFLN4, commonly used as a molecular fingerprint in force spectroscopy, and for the large, multidomain dimeric protein von Willebrand factor (VWF) that is critically involved in primary hemostasis. For both proteins, our measurements reveal exponential force dependencies of unfolding and refolding rates. We directly resolve the stabilization of the VWF A2 domain by Ca2+ and discover transitions in the VWF C domain stem at low forces that likely constitute the first steps of VWF's mechano-activation. Probing the force-dependent lifetime of biotin-streptavidin bonds, we find that monovalent streptavidin constructs with specific attachment geometry are significantly more force stable than commercial, multivalent streptavidin. We expect our modular approach to enable multiplexed force-spectroscopy measurements for a wide range of proteins, in particular in the physiologically relevant low-force regime.
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45
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Erlich KR, Sedlak SM, Jobst MA, Milles LF, Gaub HE. DNA-free directed assembly in single-molecule cut-and-paste. NANOSCALE 2019; 11:407-411. [PMID: 30604815 DOI: 10.1039/c8nr08636b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single-molecule cut-and-paste facilitates bottom-up directed assembly of nanoscale biomolecular networks in defined geometries and enables analysis with spatio-temporal resolution. However, arrangement of diverse molecules of interest requires versatile handling systems. The novel DNA-free, genetically encodable scheme described here utilises an orthogonal handling strategy to promote arrangement of enzymes and enzyme networks.
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Affiliation(s)
- Katherine R Erlich
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799 München, Germany.
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