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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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Kraka E, Quintano M, La Force HW, Antonio JJ, Freindorf M. The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena. J Phys Chem A 2022; 126:8781-8798. [DOI: 10.1021/acs.jpca.2c05962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Mateus Quintano
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Hunter W. La Force
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Juliana J. Antonio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Ave, Dallas, Texas75275-0314, United States
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Ding X, Wang Z, Zheng B, Shi S, Deng Y, Yu H, Zheng P. One-step asparaginyl endopeptidase ( OaAEP1)-based protein immobilization for single-molecule force spectroscopy. RSC Chem Biol 2022; 3:1276-1281. [PMID: 36320890 PMCID: PMC9533667 DOI: 10.1039/d2cb00135g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/18/2022] [Indexed: 11/22/2022] Open
Abstract
Enzymatic protein ligation has become the most powerful and widely used method for high-precision atomic force microscopy single-molecule force spectroscopy (AFM-SMFS) study of protein mechanics. However, this methodology typically requires the functionalization of the glass surface with a corresponding peptide sequence/tag for enzymatic recognition and multiple steps are needed. Thus, it is time-consuming and a high level of experience is needed for reliable results. To solve this problem, we simplified the procedure using two strategies both based on asparaginyl endopeptidase (AEP). First, we designed a heterobifunctional peptide-based crosslinker, GL-peptide-propargylglycine, which links to an N 3-functionalized surface via the click reaction. Then, the target protein with a C-terminal NGL sequence can be immobilized via the AEP-mediated ligation. Furthermore, we took advantage of the direct ligation between primary amino in a small molecule and protein with C-terminal NGL by AEP. Thus, the target protein can be immobilized on an amino-functionalized surface via AEP in one step. Both approaches were successfully applied to the AFM-SMFS study of eGFP, showing consistent single-molecule results.
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Affiliation(s)
- Xuan Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University 163 Xianlin Road Nanjing Jiangsu 210023 P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, 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
| | - 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
| | - Shengchao Shi
- 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
| | - Yibing 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
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University 163 Xianlin Road 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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Interdomain Linker Effect on the Mechanical Stability of Ig Domains in Titin. Int J Mol Sci 2022; 23:ijms23179836. [PMID: 36077234 PMCID: PMC9456048 DOI: 10.3390/ijms23179836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
Titin is the largest protein in humans, composed of more than one hundred immunoglobulin (Ig) domains, and plays a critical role in muscle’s passive elasticity. Thus, the molecular design of this giant polyprotein is responsible for its mechanical function. Interestingly, most of these Ig domains are connected directly with very few interdomain residues/linker, which suggests such a design is necessary for its mechanical stability. To understand this design, we chose six representative Ig domains in titin and added nine glycine residues (9G) as an artificial interdomain linker between these Ig domains. We measured their mechanical stabilities using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) and compared them to the natural sequence. The AFM results showed that the linker affected the mechanical stability of Ig domains. The linker mostly reduces its mechanical stability to a moderate extent, but the opposite situation can happen. Thus, this effect is very complex and may depend on each particular domain’s property.
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Ma Q, Lei H, Cao Y. Intramolecular covalent bonds in Gram-positive bacterial surface proteins. Chembiochem 2022; 23:e202200316. [PMID: 35801833 DOI: 10.1002/cbic.202200316] [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: 06/03/2022] [Revised: 07/07/2022] [Indexed: 11/09/2022]
Abstract
Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.
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Affiliation(s)
- Quan Ma
- Nanjing University, Department of Physics, CHINA
| | - Hai Lei
- Nanjing University, Department of Physics, CHINA
| | - Yi Cao
- Nanjing University, Department of Physics, 22 Hankou Road, 210093, Nanjing, CHINA
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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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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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