1
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Sheikhzadeh A, Safaei M, Fadaei Naeini V, Baghani M, Foroutan M, Baniassadi M. Multiscale modeling of unfolding and bond dissociation of rubredoxin metalloprotein. J Mol Graph Model 2024; 129:108749. [PMID: 38442439 DOI: 10.1016/j.jmgm.2024.108749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Mechanical properties of proteins that have a crucial effect on their operation. This study used a molecular dynamics simulation package to investigate rubredoxin unfolding on the atomic scale. Different simulation techniques were applied, and due to the dissociation of covalent/hydrogen bonds, this protein demonstrates several intermediate states in force-extension behavior. A conceptual model based on the cohesive finite element method was developed to consider the intermediate damages that occur during unfolding. This model is based on force-displacement curves derived from molecular dynamics results. The proposed conceptual model is designed to accurately identify bond rupture points and determine the associated forces. This is achieved by conducting a thorough comparison between molecular dynamics and cohesive finite element results. The utilization of a viscoelastic cohesive zone model allows for the consideration of loading rate effects. This rate-dependent model can be further developed and integrated into the multiscale modeling of large assemblies of metalloproteins, providing a comprehensive understanding of mechanical behavior while maintaining a reduced computational cost.
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Affiliation(s)
- Aliakbar Sheikhzadeh
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Mohammad Safaei
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Vahid Fadaei Naeini
- Division of Machine Elements, Luleå University of Technology, Luleå, SE-97187, Sweden
| | - Mostafa Baghani
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Masumeh Foroutan
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Majid Baniassadi
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran; University of Strasbourg, CNRS, ICUBE Laboratory, Strasbourg, France.
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2
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Wang Z, Wang M, Zhao Z, Zheng P. Quantification of carboxylate-bridged di-zinc site stability in protein due ferri by single-molecule force spectroscopy. Protein Sci 2023; 32:e4583. [PMID: 36718829 PMCID: PMC9926469 DOI: 10.1002/pro.4583] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/16/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Carboxylate-bridged diiron proteins belong to a protein family involved in different physiological processes. These proteins share the conservative EXXH motif, which provides the carboxylate bridge and is critical for metal binding. Here, we choose de novo-designed single-chain due ferri protein (DFsc), a four-helical protein with two EXXH motifs as a model protein, to study the stability of the carboxylate-bridged di-metal binding site. The mechanical and kinetic properties of the di-Zn site in DFsc were obtained by atomic force microscopy-based single-molecule force spectroscopy. Zn-DFsc showed a considerable rupture force of ~200 pN, while the apo-protein is mechanically labile. In addition, multiple rupture pathways were observed with different probabilities, indicating the importance of the EXXH-based carboxylate-bridged metal site. These results demonstrate carboxylate-bridged di-metal site is mechanically stable and improve our understanding of this important type of metalloprotein.
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Affiliation(s)
- Zhiyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Mengdie Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Zhongxin Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical EngineeringNanjing UniversityNanjingPeople's Republic of China
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3
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Li H. Single Molecule Force Spectroscopy Studies on Metalloproteins: Opportunities and Challenges. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1345-1353. [PMID: 36647634 DOI: 10.1021/acs.langmuir.2c03332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Metalloproteins play important roles in a wide range of biological processes. Elucidating the mechanisms via which metalloproteins fold and constitute their metal centers is critical to the understanding of the functions and dynamics of metalloproteins. Owing to its superior force and length resolution, single-molecule force spectroscopy (SMFS) has evolved into a powerful tool to probe the unfolding and folding mechanisms of metalloproteins at the single level by forcing metalloproteins to unfold and then refold along a reaction coordinate defined by the applied stretching force. The folding of metalloproteins is complex and involves two interwound processes, the folding of the polypeptide chain and the constitution of the metal center. Experimental studies of the folding of metalloproteins are challenging. SMFS studies have allowed researchers to directly probe the folding and unfolding of metalloproteins at the single-molecule level and the effect of metal centers on the folding-unfolding energy landscape of metalloproteins. New mechanistic insights on the folding and unfolding of some metalloproteins have been obtained, demonstrating the power and unique advantages that SMFS techniques may offer. In this Perspective, using calcium-binding proteins and small iron-sulfur proteins as examples, I provide a concise overview of the information and insights that SMFS studies have provided to understand the folding and unfolding of metalloproteins. I also discuss the opportunities and challenges that are present in this fast-progressing area of research.
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Affiliation(s)
- Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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4
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Nie JY, Song GB, Deng YB, Zheng P. Single-Molecule Force Spectroscopy Reveals Stability of mitoNEET and its [2Fe2Se] Cluster in Weakly Acidic and Basic Solutions. Chemistry 2022; 11:e202200056. [PMID: 35608094 PMCID: PMC9127745 DOI: 10.1002/open.202200056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/21/2022] [Indexed: 11/05/2022]
Abstract
The outer mitochondrial membrane protein mitoNEET (mNT) is a recently identified iron-sulfur protein containing a unique Fe2 S2 (His)1 (Cys)3 metal cluster with a single Fe-N(His87) coordinating bond. This labile Fe-N bond led to multiple unfolding/rupture pathways of mNT and its cluster by atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), one of most common tools for characterizing the molecular mechanics. Although previous ensemble studies showed that this labile Fe-N(His) bond is essential for protein function, they also indicated that the protein and its [2Fe2S] cluster are stable under acidic conditions. Thus, we applied AFM-SMFS to measure the stability of mNT and its cluster at pH values of 6, 7, and 8. Indeed, all previous multiple unfolding pathways of mNT were still observed. Moreover, single-molecule measurements revealed that the stabilities of the protein and the [2Fe2S] cluster are consistent at these pH values with only ≈20 pN force differences. Thus, we found that the behavior of the protein is consistent in both weakly acidic and basic solutions despite a labile Fe-N bond.
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Affiliation(s)
- Jing-Yuan 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
| | - Guo-Bin Song
- 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
| | - Yi-Bing Deng
- 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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5
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Nandi T, Ainavarapu SRK. Native Salt Bridges Are a Key Regulator of Ubiquitin's Mechanical Stability. J Phys Chem B 2022; 126:3505-3511. [PMID: 35535497 DOI: 10.1021/acs.jpcb.2c00972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although it is known that various intramolecular interactions determine protein mechanical stability, a detailed molecular-level understanding of the key regulators of protein mechanical stability is still lacking. Here, we present evidence for salt bridges in ubiquitin as important intramolecular interactions that can affect protein mechanical stability. Ubiquitin has two salt bridges: one relatively surface-exposed (SB1:K11-E34) and the other relatively buried (SB2:K27-D52). Ubiquitin is a reversible post-translational modifier and is stable mechanically (Favgu = 185 pN). On breaking SB1, the mechanical stability of ubiquitin is slightly enhanced (Favgu = 193 pN). In contrast, the mechanical stability significantly decreased upon breaking SB2 (Favgu = 158 pN). These results suggest that SB1 are SB2 are regulators of the mechanical stability of ubiquitin. Interestingly, the mechanical stability decreased further (Favgu = 145 pN) for the double salt bridge (DB) null variant. Monte Carlo simulations elucidate that the main regulating factor is the spontaneous unfolding rate constant (ku0), being the highest for the DB null variant followed by the SB2 null variant, and it remains unaltered for the SB1 null variant, while the native-to-transition-state distance (xu) remains unchanged. Our study provides mechanistic understanding on how two native salt bridges can independently regulate the mechanical stability in a protein, which has implications in designing protein-based robust biomaterials in the future.
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Affiliation(s)
- Tathagata Nandi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, India
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6
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Shi S, Wu T, Zheng P. Direct Measurements of the Cobalt-thiolate Bonds Strength in Rubredoxin by Single-Molecule Force Spectroscopy. Chembiochem 2022; 23:e202200165. [PMID: 35475313 DOI: 10.1002/cbic.202200165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/26/2022] [Indexed: 11/07/2022]
Abstract
Cobalt is a trace transition metal. Although it is not abundant on earth, tens of cobalt-containing proteins exist in life. Moreover, the characteristic spectrum of Co(II) ion makes it a powerful probe for the characterization of metal-binding proteins through the formation of cobalt-ligand bonds. Since most of these natural and artificial cobalt-containing proteins are stable, we believe that these cobalt-ligand bonds in the protein system are also mechanically stable. To prove this, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to directly measure the rupture force of Co(II)-thiolate bond in Co-substituted rubredoxin (CoRD). By combining the chemical denature/renature method for building metalloprotein and cysteine coupling-based polyprotein construction strategy, we successfully prepared the polyprotein sample (CoRD) n suitable for single-molecule study. Thus, we quantified the strength of Co(II)-thiolate bonds in rubredoxin with a rupture force of ~140 pN, revealing that the bond is a stable chemical bond. In addition, the Co-S bond is more labile than the Zn-S bond in proteins, similar to the result from the metal-competing titration experiment.
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Affiliation(s)
- Shengchao Shi
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Tao Wu
- Nanjing University, School of Chemistry and Chemical Engineering, CHINA
| | - Peng Zheng
- Nanjing University, School of Chemistry and Chemical Engineering, 168 Xianlin Ave, Nanjing, Jiangsu Province, 210023, Nanjing, CHINA
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7
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Li J, Li H. New insights into the folding–unfolding mechanism and conformations of cytochrome C. Chem Sci 2022; 13:7498-7508. [PMID: 35872809 PMCID: PMC9241957 DOI: 10.1039/d2sc01126c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/29/2022] [Indexed: 11/21/2022] Open
Abstract
Optical trapping experiments offer new insights into the folding and unfolding of cytochrome C.
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Affiliation(s)
- Jiayu Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
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8
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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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9
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Li J, Li H. Single molecule force spectroscopy reveals that a two-coordinate ferric site is critical for the folding of holo-rubredoxin. NANOSCALE 2020; 12:22564-22573. [PMID: 33169779 DOI: 10.1039/d0nr06275h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metalloproteins play important roles in a wide range of biological processes. The folding process of metalloproteins is complex due to the synergistic effects of the folding of their polypeptide chains and the incorporation of metal cofactors. The folding mechanism of the simplest iron-sulfur protein rubredoxin, which contains one ferric ion coordinated by four cysteinyl sulfurs, is revealed using optical tweezers for the first time. The folding of the rubredoxin polypeptide chain is rapid and robust, while the reconstitution of the iron-sulfur center is greatly dependent upon the coordination state of the ferric ion on the unfolded polypeptide chain. If the ferric ion is coordinated by two neighboring cysteines, rubredoxin can readily fold with the iron-sulfur center fully reconstituted. However, if the ferric ion is only mono-coordinated, rubredoxin can fold but the iron-sulfur center is not reconstituted. Our results suggested that the folding of holo-rubredoxin follows a novel binding-folding-reconstitution mechanism, which is distinct from the folding mechanisms proposed for the folding of metalloproteins. Our study highlights the critical importance of the two-coordinate ferric site in the folding of holo-rubredoxin, which may have some important implications to our understanding of the folding mechanism of more complex metalloproteins in vivo.
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Affiliation(s)
- Jiayu Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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10
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Song G, Ding X, Liu H, Yuan G, Tian F, Shi S, Yang Y, Li G, Zheng P. Single-Molecule Force Spectroscopy Reveals that the Fe-N Bond Enables Multiple Rupture Pathways of the 2Fe2S Cluster in a MitoNEET Monomer. Anal Chem 2020; 92:14783-14789. [PMID: 33048522 DOI: 10.1021/acs.analchem.0c03536] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mitochondrial outer membrane protein, mitoNEET (mNT), is an iron-sulfur protein containing an Fe2S2(His)1(Cys)3 cluster with a unique single Fe-N bond. Previous studies have shown that this Fe(III)-N(His) bond is essential for metal cluster transfer and protein function. To further understand the effect of this unique Fe-N bond on the metal cluster and protein, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to investigate the mechanical unfolding mechanism of an mNT monomer, focusing on the rupture pathway and kinetic stability of the cluster. We found that the Fe-N bond was the weakest point of the cluster, the rupture of which occurred first, and could be independent of the cluster break. Moreover, this Fe-N bond enabled a dynamic and labile iron-sulfur cluster, as multiple unfolding pathways of mNT with a unique Fe2S2(Cys)3 intermediate were observed accordingly.
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Affiliation(s)
- Guobin Song
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Xuan Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Huaxing Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Guodong Yuan
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, 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, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Yang Yang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Guoqiang Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center, 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, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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11
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Liu Z, Liu H, Vera AM, Bernardi RC, Tinnefeld P, Nash MA. High force catch bond mechanism of bacterial adhesion in the human gut. Nat Commun 2020; 11:4321. [PMID: 32859904 PMCID: PMC7456326 DOI: 10.1038/s41467-020-18063-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022] Open
Abstract
Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble substrates under hydrodynamic flow. Here we report the molecular mechanism behind an ultrastable protein complex responsible for resisting shear forces and adhering bacteria to cellulose fibers in the human gut. Using single-molecule force spectroscopy (SMFS), single-molecule FRET (smFRET), and molecular dynamics (MD) simulations, we resolve two binding modes and three unbinding reaction pathways of a mechanically ultrastable R. champanellensis (Rc) Dockerin:Cohesin (Doc:Coh) complex. The complex assembles in two discrete binding modes with significantly different mechanical properties, with one breaking at ~500 pN and the other at ~200 pN at loading rates from 1-100 nN s-1. A neighboring X-module domain allosterically regulates the binding interaction and inhibits one of the low-force pathways at high loading rates, giving rise to a catch bonding mechanism that manifests under force ramp protocols. Multi-state Monte Carlo simulations show strong agreement with experimental results, validating the proposed kinetic scheme. These results explain mechanistically how gut microbes regulate cell adhesion strength at high shear stress through intricate molecular mechanisms including dual-binding modes, mechanical allostery and catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
- Department of Physics, Auburn University, 36849, Auburn, AL, USA
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
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12
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Li Y, Cheng J, Delparastan P, Wang H, Sigg SJ, DeFrates KG, Cao Y, Messersmith PB. Molecular design principles of Lysine-DOPA wet adhesion. Nat Commun 2020; 11:3895. [PMID: 32753588 PMCID: PMC7403305 DOI: 10.1038/s41467-020-17597-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023] Open
Abstract
The mussel byssus has long been a source of inspiration for the adhesion community. Recently, adhesive synergy between flanking lysine (Lys, K) and 3,4-Dihydroxyphenylalanine (DOPA, Y) residues in the mussel foot proteins (Mfps) has been highlighted. However, the complex topological relationship of DOPA and Lys as well as the interfacial adhesive roles of other amino acids have been understudied. Herein, we study adhesion of Lys and DOPA-containing peptides to organic and inorganic substrates using single-molecule force spectroscopy (SMFS). We show that a modest increase in peptide length, from KY to (KY)3, increases adhesion strength to TiO2. Surprisingly, further increase in peptide length offers no additional benefit. Additionally, comparison of adhesion of dipeptides containing Lys and either DOPA (KY) or phenylalanine (KF) shows that DOPA is stronger and more versatile. We furthermore demonstrate that incorporating a nonadhesive spacer between (KY) repeats can mimic the hidden length in the Mfp and act as an effective strategy to dissipate energy.
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Affiliation(s)
- Yiran Li
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
- Department of Physics, Nanjing University, 210093, Nanjing, P. R. China
| | - Jing Cheng
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
| | - Peyman Delparastan
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
| | - Haoqi Wang
- Department of Physics, Nanjing University, 210093, Nanjing, P. R. China
| | - Severin J Sigg
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
| | - Kelsey G DeFrates
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA
| | - Yi Cao
- Department of Physics, Nanjing University, 210093, Nanjing, P. R. China
| | - Phillip B Messersmith
- Departments of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA.
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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13
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Scheurer M, Dreuw A, Head-Gordon M, Stauch T. The rupture mechanism of rubredoxin is more complex than previously thought. Chem Sci 2020; 11:6036-6044. [PMID: 34094096 PMCID: PMC8159389 DOI: 10.1039/d0sc02164d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The surprisingly low rupture force and remarkable mechanical anisotropy of rubredoxin have been known for several years. Exploiting the first combination of steered molecular dynamics and the quantum chemical Judgement of Energy DIstribution (JEDI) analysis, the common belief that hydrogen bonds between neighboring amino acid backbones and the sulfur atoms of the central FeS4 unit in rubredoxin determine the low mechanical resistance of the protein is invalidated. The distribution of strain energy in the central part of rubredoxin is elucidated in real-time with unprecedented detail, giving important insights into the mechanical unfolding pathway of rubredoxin. While structural anisotropy as well as the contribution of angle bendings in the FeS4 unit have a significant influence on the mechanical properties of rubredoxin, these factors are insufficient to explain the experimentally observed low rupture force. Instead, the rupture mechanism of rubredoxin is far more complex than previously thought and requires more than just a hydrogen bond network.
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Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific ComputingIm Neuenheimer Feld 20569120 HeidelbergGermany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific ComputingIm Neuenheimer Feld 20569120 HeidelbergGermany
| | - Martin Head-Gordon
- Department of Chemistry, University of CaliforniaBerkeleyCalifornia 94720USA,Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of CaliforniaBerkeleyCalifornia 94720USA
| | - Tim Stauch
- University of Bremen, Institute for Physical and Theoretical ChemistryLeobener Straße NW2D-28359 BremenGermany,Bremen Center for Computational Materials Science, University of BremenAm Fallturm 1D-28359 BremenGermany,MAPEX Center for Materials and Processes, University of BremenBibliothekstraße 1D-28359 BremenGermany
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14
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Jehle F, Macías-Sánchez E, Sviben S, Fratzl P, Bertinetti L, Harrington MJ. Hierarchically-structured metalloprotein composite coatings biofabricated from co-existing condensed liquid phases. Nat Commun 2020; 11:862. [PMID: 32054841 PMCID: PMC7018715 DOI: 10.1038/s41467-020-14709-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/24/2020] [Indexed: 12/16/2022] Open
Abstract
Complex hierarchical structure governs emergent properties in biopolymeric materials; yet, the material processing involved remains poorly understood. Here, we investigated the multi-scale structure and composition of the mussel byssus cuticle before, during and after formation to gain insight into the processing of this hard, yet extensible metal cross-linked protein composite. Our findings reveal that the granular substructure crucial to the cuticle’s function as a wear-resistant coating of an extensible polymer fiber is pre-organized in condensed liquid phase secretory vesicles. These are phase-separated into DOPA-rich proto-granules enveloped in a sulfur-rich proto-matrix which fuses during secretion, forming the sub-structure of the cuticle. Metal ions are added subsequently in a site-specific way, with iron contained in the sulfur-rich matrix and vanadium coordinated by DOPA-catechol in the granule. We posit that this hierarchical structure self-organizes via phase separation of specific amphiphilic proteins within secretory vesicles, resulting in a meso-scale structuring that governs cuticle function. The mussel byssus cuticle is a wear-resistant and extensible metalloprotein composite. Here, the authors probed the cuticle nanostructure and composition before, during and after fabrication revealing a crucial role of metal-binding proteins that self-organize via liquid-liquid phase separation.
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Affiliation(s)
- Franziska Jehle
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
| | - Elena Macías-Sánchez
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
| | - Sanja Sviben
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
| | - Peter Fratzl
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
| | - Luca Bertinetti
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.
| | - Matthew J Harrington
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany. .,Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, QC, H3A 0B8, Canada.
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15
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Dudev T, Frutos LM, Castaño O. How mechanical forces can modulate the metal affinity and selectivity of metal binding sites in proteins. Metallomics 2020; 12:363-370. [DOI: 10.1039/c9mt00283a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The results obtained reveal that applying mechanical forces with a given strength and directionality can modulate the metal affinity and selectivity of metal binding sites in metalloproteins.
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Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy
- Sofia University
- 1164 Sofia
- Bulgaria
| | - Luis Manuel Frutos
- Departamento de Química Analítica
- Química Física e Ingeniería Química
- Universidad de Alcala
- Madrid
- Spain
| | - Obis Castaño
- Departamento de Química Analítica
- Química Física e Ingeniería Química
- Universidad de Alcala
- Madrid
- Spain
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16
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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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