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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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Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
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Chen R, Luo C. Stretching effect on intrachain conformational ordering of polymers: A steered molecular dynamics simulation. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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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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Xu Y, Kang R, Ren L, Yang L, Yue T. Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations. Biomolecules 2021; 11:1688. [PMID: 34827686 PMCID: PMC8615548 DOI: 10.3390/biom11111688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
The knot is one of the most remarkable topological features identified in an increasing number of proteins with important functions. However, little is known about how the knot is formed during protein folding, and untied or maintained in protein unfolding. By means of all-atom molecular dynamics simulation, here we employ methyltransferase YbeA as the knotted protein model to analyze changes of the knotted conformation coupled with protein unfolding under thermal and mechanical denaturing conditions. Our results show that the trefoil knot in YbeA is occasionally untied via knot loosening rather than sliding under enhanced thermal fluctuations. Through correlating protein unfolding with changes in the knot position and size, several aspects of barriers that jointly suppress knot untying are revealed. In particular, protein unfolding is always prior to knot untying and starts preferentially from separation of two α-helices (α1 and α5), which protect the hydrophobic core consisting of β-sheets (β1-β4) from exposure to water. These β-sheets form a loop through which α5 is threaded to form the knot. Hydrophobic and hydrogen bonding interactions inside the core stabilize the loop against loosening. In addition, residues at N-terminal of α5 define a rigid turning to impede α5 from sliding out of the loop. Site mutations are designed to specifically eliminate these barriers, and easier knot untying is achieved under the same denaturing conditions. These results provide new molecular level insights into the folding/unfolding of knotted proteins.
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Affiliation(s)
- Yan Xu
- College of Electronic Engineering and Automation, Shandong University of Science and Technology, Qingdao 266590, China;
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China;
| | - Runshan Kang
- College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China;
| | - Luyao Ren
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
| | - Lin Yang
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
| | - Tongtao Yue
- Key Laboratory of Marine Environment and Ecology, Institute of Coastal Environmental Pollution Control, Ministry of Education, College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; (L.R.); (L.Y.)
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Bauer J, Žoldák G. Interpretation of Single-Molecule Force Experiments on Proteins Using Normal Mode Analysis. NANOMATERIALS 2021; 11:nano11112795. [PMID: 34835560 PMCID: PMC8624234 DOI: 10.3390/nano11112795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
Single-molecule force spectroscopy experiments allow protein folding and unfolding to be explored using mechanical force. Probably the most informative technique for interpreting the results of these experiments at the structural level makes use of steered molecular dynamics (MD) simulations, which can explicitly model the protein under load. Unfortunately, this technique is computationally expensive for many of the most interesting biological molecules. Here, we find that normal mode analysis (NMA), a significantly cheaper technique from a computational perspective, allows at least some of the insights provided by MD simulation to be gathered. We apply this technique to three non-homologous proteins that were previously studied by force spectroscopy: T4 lysozyme (T4L), Hsp70 and the glucocorticoid receptor domain (GCR). The NMA results for T4L and Hsp70 are compared with steered MD simulations conducted previously, and we find that we can recover the main results. For the GCR, which did not undergo MD simulation, our approach identifies substructures that correlate with experimentally identified unfolding intermediates. Overall, we find that NMA can make a valuable addition to the analysis toolkit for the structural analysis of single-molecule force experiments on proteins.
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Affiliation(s)
- Jacob Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
- Correspondence: (J.B.); (G.Ž.); Tel.: +421-55-234-2242 (G.Ž.)
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, Technology and Innovation Park, Trieda SNP 1, 041 54 Košice, Slovakia
- Correspondence: (J.B.); (G.Ž.); Tel.: +421-55-234-2242 (G.Ž.)
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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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Paissoni C, Puri S, Wang I, Chen SY, Camilloni C, Hsu STD. Converging experimental and computational views of the knotting mechanism of a small knotted protein. Biophys J 2021; 120:2276-2286. [PMID: 33812848 PMCID: PMC8390826 DOI: 10.1016/j.bpj.2021.03.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/14/2021] [Accepted: 03/29/2021] [Indexed: 01/18/2023] Open
Abstract
MJ0366 from Methanocaldococcus jannaschii is the smallest topologically knotted protein known to date. 92 residues in length, MJ0366 ties a trefoil (31) knot by threading its C-terminal helix through a buttonhole formed by the remainder of the secondary structure elements. By generating a library of point mutations at positions pertinent to the knot formation, we systematically evaluated the contributions of individual residues to the folding stability and kinetics of MJ0366. The experimental Φ-values were used as restraints to computationally generate an ensemble of conformations that correspond to the transition state of MJ0366, which revealed several nonnative contacts. The importance of these nonnative contacts in stabilizing the transition state of MJ0366 was confirmed by a second round of mutagenesis, which also established the pivotal role of F15 in stapling the network of hydrophobic interactions around the threading C-terminal helix. Our converging experimental and computational results show that, despite the small size, the transition state of MJ0366 is formed at a very late stage of the folding reaction coordinate, following a polarized pathway. Eventually, the formation of extensive native contacts, as well as a number of nonnative ones, leads to the threading of the C-terminal helix that defines the topological knot.
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Affiliation(s)
- Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Sarita Puri
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Iren Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Szu-Yu Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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Motta S, Pandini A, Fornili A, Bonati L. Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks. J Chem Theory Comput 2021; 17:2080-2089. [PMID: 33780250 PMCID: PMC8047803 DOI: 10.1021/acs.jctc.0c01308] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Several experimental
studies indicated that large conformational
changes, including partial domain unfolding, have a role in the functional
mechanisms of the basic helix loop helix Per/ARNT/SIM (bHLH-PAS) transcription
factors. Recently, single-molecule atomic force microscopy (AFM) revealed
two distinct pathways for the mechanical unfolding of the ARNT PAS-B.
In this work we used steered molecular dynamics simulations to gain
new insights into this process at an atomistic level. To reconstruct
and classify pathways sampled in multiple simulations, we designed
an original approach based on the use of self-organizing maps (SOMs).
This led us to identify two types of unfolding pathways for the ARNT
PAS-B, which are in good agreement with the AFM findings. Analysis
of average forces mapped on the SOM revealed a stable conformation
of the PAS-B along one pathway, which represents a possible structural
model for the intermediate state detected by AFM. The approach here
proposed will facilitate the study of other signal transmission mechanisms
involving the folding/unfolding of PAS domains.
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Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Alessandro Pandini
- Department of Computer Science, Brunel University London, Uxbridge UB8 3PH, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
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Abstract
Multiple gram-negative bacteria encode type III secretion systems (T3SS) that allow them to inject effector proteins directly into host cells to facilitate colonization. To be secreted, effector proteins must be at least partially unfolded to pass through the narrow needle-like channel (diameter <2 nm) of the T3SS. Fusion of effector proteins to tightly packed proteins-such as GFP, ubiquitin, or dihydrofolate reductase (DHFR)-impairs secretion and results in obstruction of the T3SS. Prior observation that unfolding can become rate-limiting for secretion has led to the model that T3SS effector proteins have low thermodynamic stability, facilitating their secretion. Here, we first show that the unfolding free energy ([Formula: see text]) of two Salmonella effector proteins, SptP and SopE2, are 6.9 and 6.0 kcal/mol, respectively, typical for globular proteins and similar to published [Formula: see text] for GFP, ubiquitin, and DHFR. Next, we mechanically unfolded individual SptP and SopE2 molecules by atomic force microscopy (AFM)-based force spectroscopy. SptP and SopE2 unfolded at low force (F unfold ≤ 17 pN at 100 nm/s), making them among the most mechanically labile proteins studied to date by AFM. Moreover, their mechanical compliance is large, as measured by the distance to the transition state (Δx ‡ = 1.6 and 1.5 nm for SptP and SopE2, respectively). In contrast, prior measurements of GFP, ubiquitin, and DHFR show them to be mechanically robust (F unfold > 80 pN) and brittle (Δx ‡ < 0.4 nm). These results suggest that effector protein unfolding by T3SS is a mechanical process and that mechanical lability facilitates efficient effector protein secretion.
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Zhang X, Chen J, Li E, Hu C, Luo SZ, He C. Ultrahigh Adhesion Force Between Silica-Binding Peptide SB7 and Glass Substrate Studied by Single-Molecule Force Spectroscopy and Molecular Dynamic Simulation. Front Chem 2020; 8:600918. [PMID: 33330393 PMCID: PMC7729015 DOI: 10.3389/fchem.2020.600918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/23/2020] [Indexed: 12/22/2022] Open
Abstract
Many proteins and peptides have been identified to effectively and specifically bind on certain surfaces such as silica, polystyrene and titanium dioxide. It is of great interest, in many areas such as enzyme immobilization, surface functionalization and nanotechnology, to understand how these proteins/peptides bind to solid surfaces. Here we use single-molecule force spectroscopy (SMFS) based on atomic force microscopy to directly measure the adhesion force between a silica-binding peptide SB7 and glass surface at single molecule level. SMFS results show that the adhesion force of a single SB7 detaching from the glass surface distributes in two populations at ~220 pN and 610 pN, which is higher than the unfolding forces of most mechanically stable proteins and the unbinding forces of most stable protein-protein interactions. Molecular dynamics simulation reveals that the electrostatic interactions between positively charged arginine residues and the silica surface dominates the binding of SB7 on silica. Our study provides experimental evidence and molecular mechanism at the single-molecule level for the SB7-based immobilization of proteins on silica-based surface, which is able to withstand high mechanical forces, making it an ideal fusion tag for silica surface immobilization or peptide-base adhesive materials.
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Affiliation(s)
- Xiaoxu Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijng, China
| | - Jialin Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Enci Li
- State Key Laboratory of Precision Measuring Technology and Instrument, Tianjin University, Tianjin, China
| | - Chunguang Hu
- State Key Laboratory of Precision Measuring Technology and Instrument, Tianjin University, Tianjin, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Chengzhi He
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijng, China
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Wang H, Li H. Mechanically tightening, untying and retying a protein trefoil knot by single-molecule force spectroscopy. Chem Sci 2020; 11:12512-12521. [PMID: 34123232 PMCID: PMC8162576 DOI: 10.1039/d0sc02796k] [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] [Indexed: 02/01/2023] Open
Abstract
Knotted conformation is one of the most surprising topological features found in proteins, and understanding the folding mechanism of such knotted proteins remains a challenge. Here, we used optical tweezers (OT) to investigate the mechanical unfolding and folding behavior of a knotted protein Escherichia coli tRNA (guanosine-1) methyltransferase (TrmD). We found that when stretched from its N- and C-termini, TrmD can be mechanically unfolded and stretched into a tightened trefoil knot, which is composed of ca. 17 residues. Stretching of the unfolded TrmD involved a compaction process of the trefoil knot at low forces. The unfolding pathways of the TrmD were bifurcated, involving two-state and three-state pathways. Upon relaxation, the tightened trefoil knot loosened up first, leading to the expansion of the knot, and the unfolded TrmD can then fold back to its native state efficiently. By using an engineered truncation TrmD variant, we stretched TrmD along a pulling direction to allow us to mechanically unfold TrmD and untie the trefoil knot. We found that the folding of TrmD from its unfolded polypeptide without the knot is significantly slower. The knotting is the rate-limiting step of the folding of TrmD. Our results highlighted the critical importance of the knot conformation for the folding and stability of TrmD, offering a new perspective to understand the role of the trefoil knot in the biological function of TrmD. Optical tweezers are used to stretch a knotted protein along different directions to probe its unfolding–folding behaviors, and the conformational change of its knot structure. ![]()
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Affiliation(s)
- Han Wang
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
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14
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Piejko M, Niewieczerzal S, Sulkowska JI. The Folding of Knotted Proteins: Distinguishing the Distinct Behavior of Shallow and Deep Knots. Isr J Chem 2020. [DOI: 10.1002/ijch.202000036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Maciej Piejko
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
| | | | - Joanna I. Sulkowska
- Faculty of ChemistryUniversity of Warsaw Pasteura 1 Warsaw 02-093 Poland
- Centre of New TechnologiesUniversity of Warsaw Banacha 2c Warsaw 02-097 Poland
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15
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Deng Y, Shi S, Zheng B, Wu T, Zheng P. Enzymatic Construction of Protein Polymer/Polyprotein Using OaAEP1 and TEV Protease. Bio Protoc 2020; 10:e3596. [PMID: 33659562 PMCID: PMC7842765 DOI: 10.21769/bioprotoc.3596] [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: 09/23/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 04/01/2024] Open
Abstract
The development of chemical and biological coupling technologies in recent years has made possible of protein polymers engineering. We have developed an enzymatic method for building polyproteins using a protein ligase OaAEP1 (asparagine endopeptidase 1) and protease TEV (tobacco etching virus). Using a mobile TEV protease site compatible with the OaAEP1 ligation, we achieved a stepwise polymerization of the protein on the surface. The produced polyprotein can be verified by protein unfolding scenario using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Thus, this study provides an alternative method for polyprotein engineering and immobilization.
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Affiliation(s)
- Yibing Deng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
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16
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Daskalakis V, Papadatos S, Stergiannakos T. The conformational phase space of the photoprotective switch in the major light harvesting complex II. Chem Commun (Camb) 2020; 56:11215-11218. [DOI: 10.1039/d0cc04486e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Extensive conformational sampling of the major light harvesting complex II defines the collective variables of the photoprotective switch.
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Affiliation(s)
- Vangelis Daskalakis
- Department of Chemical Engineering
- Cyprus University of Technology
- 3603 Limassol
- Cyprus
| | - Sotiris Papadatos
- Department of Chemical Engineering
- Cyprus University of Technology
- 3603 Limassol
- Cyprus
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17
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Perego C, Potestio R. Computational methods in the study of self-entangled proteins: a critical appraisal. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:443001. [PMID: 31269476 DOI: 10.1088/1361-648x/ab2f19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The existence of self-entangled proteins, the native structure of which features a complex topology, unveils puzzling, and thus fascinating, aspects of protein biology and evolution. The discovery that a polypeptide chain can encode the capability to self-entangle in an efficient and reproducible way during folding, has raised many questions, regarding the possible function of these knots, their conservation along evolution, and their role in the folding paradigm. Understanding the function and origin of these entanglements would lead to deep implications in protein science, and this has stimulated the scientific community to investigate self-entangled proteins for decades by now. In this endeavour, advanced experimental techniques are more and more supported by computational approaches, that can provide theoretical guidelines for the interpretation of experimental results, and for the effective design of new experiments. In this review we provide an introduction to the computational study of self-entangled proteins, focusing in particular on the methodological developments related to this research field. A comprehensive collection of techniques is gathered, ranging from knot theory algorithms, that allow detection and classification of protein topology, to Monte Carlo or molecular dynamics strategies, that constitute crucial instruments for investigating thermodynamics and kinetics of this class of proteins.
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Affiliation(s)
- Claudio Perego
- Max Panck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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18
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Daskalakis V, Maity S, Hart CL, Stergiannakos T, Duffy CDP, Kleinekathöfer U. Structural Basis for Allosteric Regulation in the Major Antenna Trimer of Photosystem II. J Phys Chem B 2019; 123:9609-9615. [DOI: 10.1021/acs.jpcb.9b09767] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vangelis Daskalakis
- Department of Environmental Science and Technology, Cyprus University of Technology, 30 Archbishop Kyprianou Street, 3603, Limassol, Cyprus
| | - Sayan Maity
- Department of Physics & Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Cameron Lewis Hart
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Taxiarchis Stergiannakos
- Department of Environmental Science and Technology, Cyprus University of Technology, 30 Archbishop Kyprianou Street, 3603, Limassol, Cyprus
| | - Christopher D. P. Duffy
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Ulrich Kleinekathöfer
- Department of Physics & Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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19
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Xu Y, Li S, Yan Z, Ge B, Huang F, Yue T. Revealing Cooperation between Knotted Conformation and Dimerization in Protein Stabilization by Molecular Dynamics Simulations. J Phys Chem Lett 2019; 10:5815-5822. [PMID: 31525988 DOI: 10.1021/acs.jpclett.9b02209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The topological knot is thought to play a stabilizing role in maintaining the global fold and nature of proteins with the underlying mechanism yet to be elucidated. Given that most proteins containing trefoil knots exist and function as homodimers with a large part of the dimer interface occupied by the knotted region, we reason that the knotted conformation cooperates with dimerization in protein stabilization. Here, we take YbeA from Escherichia coli as the knotted protein model, using molecular dynamics (MD) simulations to compare the stability of two pairs of dimeric proteins having the same sequence and secondary structures but differing in the presence or absence of a trefoil knot in each subunit. The dimer interface of YbeA is identified to involve favorable contacts among three α-helices (α1, α3, and α5), one of which (α5) is threaded through a loop connected with α3 to form the knot. Upon removal of the knot by appropriate change of the knot-making crossing of the polypeptide chain, relevant domains are less constrained and exhibit enhanced fluctuations to decrease contacts at the interface. Unknotted subunits are less compact and undergo structural changes to ease the dimer separation. Such a stabilizing effect is evidenced by steered MD simulations, showing that the mechanical force required for dimer separation is significantly reduced by removing the knot. In addition to the knotted conformation, dimerization further improves the protein stability by restricting the α1-α5 separation, which is defined as a leading step for protein unfolding. These results provide important insights into the structure-function relationship of dimerization in knotted proteins.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
- College of Electronic Engineering and Automation , Shandong University of Science and Technology , Qingdao 266590 , China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Zengshuai Yan
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering , China University of Petroleum (East China) , Qingdao 266580 , China
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20
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Fine tuning of the photosystem II major antenna mobility within the thylakoid membrane of higher plants. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183059. [PMID: 31518553 DOI: 10.1016/j.bbamem.2019.183059] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/16/2019] [Accepted: 09/04/2019] [Indexed: 12/15/2022]
Abstract
Depending on the amount of light, the photosystem II (PSII) antennae or Light Harvesting Complexes (LHCII) switch between two states within the thylakoid membranes of higher plants, i.e., a light-harvesting and a photoprotective mode. This switch is co-regulated by a pH gradient (ΔpH) across the membrane and the interaction with the PSII subunit S (PsbS) that is proposed to induce LHCII aggregation. Herein we employ all-atom and coarse-grained molecular simulations of the major LHCII trimer at low and excess ΔpH, as well as in complexation with PsbS within a native thylakoid membrane model. Our results demonstrate the aggregation potential of LHCII and, consistent with the experimental literature, reveal the role of PsbS at atomic resolution. PsbS alters the LHCII-thylakoid lipid interactions and restores the LHCII mobility that is lost in the transition to photoprotective conditions (low lumenal pH). In agreement with this finding, diffusion of the integral membrane protein LHCII is dependent on both, electrostatic interactions and hydrophobic mismatch, while it does not obey the Saffman-Delbrück diffusion model.
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21
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Yuan G, Ma Q, Wu T, Wang M, Li X, Zuo J, Zheng P. Multistep Protein Unfolding Scenarios from the Rupture of a Complex Metal Cluster Cd 3S 9. Sci Rep 2019; 9:10518. [PMID: 31324867 PMCID: PMC6642161 DOI: 10.1038/s41598-019-47004-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
Protein (un)folding is a complex and essential process. With the rapid development of single-molecule techniques, we can detect multiple and transient proteins (un)folding pathways/intermediates. However, the observation of multiple multistep (>2) unfolding scenarios for a single protein domain remains limited. Here, we chose metalloprotein with relatively stable and multiple metal-ligand coordination bonds as a system for such a purpose. Using AFM-based single-molecule force spectroscopy (SMFS), we successfully demonstrated the complex and multistep protein unfolding scenarios of the β-domain of a human protein metallothionein-3 (MT). MT is a protein of ~60 amino acids (aa) in length with 20 cysteines for various metal binding, and the β-domain (βMT) is of ~30 aa with an M3S9 metal cluster. We detected four different types of three-step protein unfolding scenarios from the Cd-βMT, which can be possibly explained by the rupture of Cd-S bonds in the complex Cd3S9 metal cluster. In addition, complex unfolding scenarios with four rupture peaks were observed. The Cd-S bonds ruptured in both single bond and multiple bonds modes. Our results provide not only evidence for multistep protein unfolding phenomena but also reveal unique properties of metalloprotein system using single-molecule AFM.
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Affiliation(s)
- Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Qun Ma
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Mengdi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Jinglin Zuo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China.
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22
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Wang H, Gao X, Hu X, Hu X, Hu C, Li H. Mechanical Unfolding and Folding of a Complex Slipknot Protein Probed by Using Optical Tweezers. Biochemistry 2019; 58:4751-4760. [DOI: 10.1021/acs.biochem.9b00320] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Han Wang
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Xiaoqing Gao
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- State Key Laboratory of Precision Measurements Technology Instruments, School of Precision Instrument Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xiaodong Hu
- State Key Laboratory of Precision Measurements Technology Instruments, School of Precision Instrument Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology Instruments, School of Precision Instrument Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Chunguang Hu
- State Key Laboratory of Precision Measurements Technology Instruments, School of Precision Instrument Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- State Key Laboratory of Precision Measurements Technology Instruments, School of Precision Instrument Optoelectronics Engineering, Tianjin University, Tianjin 300072, People’s Republic of China
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23
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He C, Li S, Gao X, Xiao A, Hu C, Hu X, Hu X, Li H. Direct observation of the fast and robust folding of a slipknotted protein by optical tweezers. NANOSCALE 2019; 11:3945-3951. [PMID: 30762052 DOI: 10.1039/c8nr10070e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding the folding mechanism of knotted and slipknotted proteins has attracted considerable interest. Due to their topological complexity, knotted and slipknotted proteins are predicted to fold slowly and involve large topological barriers. Molecular dynamics simulation studies suggest that a slipknotted conformation can serve as an important intermediate to help greatly reduce the topological difficulty during the folding of some knotted proteins. Here we use a single molecule optical tweezers technique to directly probe the folding of a small slipknotted protein AFV3-109. We found that stretching AFV3-109 can lead to the untying of the slipknot and complete unfolding of AFV3-109. Upon relaxation, AFV3-109 can readily refold back to its native slipknot conformation with high fidelity when the stretching force is lower than 6 pN. The refolding of AFV3-109 occurs in a sharp two-state like transition. Our results indicate that, different from knotted proteins, the folding of a slipknotted protein like AFV3-109 can be fast, and may not necessarily involve a high topological barrier.
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Affiliation(s)
- Chengzhi He
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Shuai Li
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Xiaoqing Gao
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Adam Xiao
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Chunguang Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Xiaodong Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Xiaotang Hu
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Nanchang Institute for Microtechnology of Tianjin University, Tianjin, 300072, P.R. China
| | - Hongbin Li
- State Key Laboratory of Precision Measuring Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072, P. R. China. and Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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24
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Xu Y, Li S, Yan Z, Luo Z, Ren H, Ge B, Huang F, Yue T. Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations. Biophys J 2018; 115:1681-1689. [PMID: 30314655 PMCID: PMC6225051 DOI: 10.1016/j.bpj.2018.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/11/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022] Open
Abstract
A growing number of proteins have been identified as knotted in their native structures, with such entangled topological features being expected to play stabilizing roles maintaining both the global fold and the nature of proteins. However, the molecular mechanism underlying the stabilizing effect is ambiguous. Here, we combine unbiased and mechanical atomistic molecular dynamics simulations to investigate how a protein is stabilized by an inherent knot by directly comparing chemical, thermal, and mechanical denaturing properties of two proteins having the same sequence and secondary structures but differing in the presence or absence of an inherent knot. One protein is YbeA from Escherichia coli, containing a deep trefoil knot within the sequence, and the other is the modified protein with the knot of YbeA being removed. Under certain chemical denaturing conditions, the unknotted protein fully unfolds whereas the knotted protein does not, suggesting a higher intrinsic stability for the protein having a knot. Both proteins unfold under enhanced thermal fluctuations but at different rates and with distinct pathways. Opening the hydrophobic core via separation between two α-helices is identified as a crucial step initiating the protein unfolding, which, however, is restrained for the knotted protein by topological and geometrical frustrations. Energy barriers for denaturing the protein are reduced by removing the knot, as evidenced by mechanical unfolding simulations. Finally, yet importantly, no obvious change in size or location of the knot was observed during denaturing processes, indicating that YbeA may remain knotted for a relatively long time during and after denaturation.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Shixin Li
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zengshuai Yan
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Zhen Luo
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Hao Ren
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Baosheng Ge
- Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China; Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, China.
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25
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Daskalakis V, Papadatos S. The Photosystem II Subunit S under Stress. Biophys J 2018; 113:2364-2372. [PMID: 29211990 DOI: 10.1016/j.bpj.2017.09.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/29/2017] [Accepted: 09/29/2017] [Indexed: 01/08/2023] Open
Abstract
Nonphotochemical quenching is the protective mechanism against overexcitation of photosystem II, triggered by excess ΔpH in photosynthetic membranes. The light-harvesting complexes (LHCs), the de-epoxidation of violaxanthin to zeaxanthin, and the photosystem II subunit S (PsbS) work in synergy for an optimized multilevel response. Understanding the fine details of this synergy has proven challenging to scientific research. Here, we employ large-scale, all-atom molecular simulations and beyond experimental insight, we proceed a step further in identifying the PsbS dynamics that could possibly be associated with this synergy. For the first time, to our knowledge, we probe the distinct behavior of PsbS under ΔpH that probes the details of the potential dimer-to-monomer transition, and in a violaxanthin/zeaxanthin-rich membrane, at an all-atom resolution. We propose that the lumen-exposed residues, threonine 162 and glutamic acid 173, form stabilizing hydrogen bonds between the PsbS monomers only at high lumen pH, whereas at low pH (excess ΔpH) this interaction is lost, and leads to higher flexibility of the protein and potentially to the dimer-to-monomer transition. Lastly, we discuss how conformational changes under the presence of ΔpH/zeaxanthin are related to the PsbS role in the current nonphotochemical quenching model in the literature. For the latter, we probe a PsbS-monomeric LHCII association. The association is proposed to potentially alter the monomeric LHCII sensitivity to ΔpH by changing the pKa values of interacting LHCII residues. This serves as an example where protonation-ligation events enhance protein-protein interactions fundamental to many life processes.
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Affiliation(s)
- Vangelis Daskalakis
- Department of Environmental Science and Technology, Cyprus University of Technology, Limassol, Cyprus.
| | - Sotiris Papadatos
- Department of Environmental Science and Technology, Cyprus University of Technology, Limassol, Cyprus
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26
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Sulkowska JI, Sułkowski P. Entangled Proteins: Knots, Slipknots, Links, and Lassos. SPRINGER SERIES IN SOLID-STATE SCIENCES 2018. [DOI: 10.1007/978-3-319-76596-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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Dabrowski-Tumanski P, Sulkowska JI. To Tie or Not to Tie? That Is the Question. Polymers (Basel) 2017; 9:E454. [PMID: 30965758 PMCID: PMC6418553 DOI: 10.3390/polym9090454] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of entangled proteins. Around 6% of protein structures deposited in the PBD are entangled, forming knots, slipknots, lassos and links. We present theoretical methods and tools that enabled discovering and classifying such structures. We discuss the advantages and disadvantages of the non-trivial topology in proteins, based on available data about folding, stability, biological properties and evolutionary conservation. We also formulate intriguing and challenging questions on the border of biophysics, bioinformatics, biology and mathematics, which arise from the discovery of an entanglement in proteins. Finally, we discuss possible applications of entangled proteins in medicine and nanotechnology, such as the chance to design super stable proteins, whose stability could be controlled by chemical potential.
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Affiliation(s)
- Pawel Dabrowski-Tumanski
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland.
| | - Joanna I Sulkowska
- Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland.
- Faculty of Chemistry, University of Warsaw, Warsaw 02-093, Poland.
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28
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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29
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Feng W, Wang Z, Zhang W. Effect of Chain Conformation on the Single-Molecule Melting Force in Polymer Single Crystals: Steered Molecular Dynamics Simulations Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:1826-1833. [PMID: 28177634 DOI: 10.1021/acs.langmuir.6b04457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain. To do that, steered molecular dynamics simulations were performed on those polymer single crystals by pulling individual polymer chains out of the crystals. Our results show that the patterns of force-extension curve as well as the chain moving mode are closely related to the conformation of the polymer chain in the single crystal. In addition, hydrogen bonds can enhance greatly the force required to stretch the polymer chain out of the single crystal. The dynamic breaking and reformation of multivalent hydrogen bonds have been observed for the first time in PA66 at the single molecule level.
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Affiliation(s)
- Wei Feng
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
- Institute of Atomic and Molecular Physics, Jilin University , Changchun 130012, P. R. China
| | - Zhigang Wang
- Institute of Atomic and Molecular Physics, Jilin University , Changchun 130012, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , 2699 Qianjin Street, Changchun 130012, P. R. China
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30
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Single-molecule force spectroscopy on polyproteins and receptor–ligand complexes: The current toolbox. J Struct Biol 2017; 197:3-12. [DOI: 10.1016/j.jsb.2016.02.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 11/21/2022]
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31
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Allen CD, Chen MY, Trick AY, Le DT, Ferguson AL, Link AJ. Thermal Unthreading of the Lasso Peptides Astexin-2 and Astexin-3. ACS Chem Biol 2016; 11:3043-3051. [PMID: 27588549 DOI: 10.1021/acschembio.6b00588] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lasso peptides are a class of knot-like polypeptides in which the C-terminal tail of the peptide threads through a ring formed by an isopeptide bond between the N-terminal amine group and a side chain carboxylic acid. The small size (∼20 amino acids) and simple topology of lasso peptides make them a good model system for studying the unthreading of entangled polypeptides, both with experiments and atomistic simulation. Here, we present an in-depth study of the thermal unthreading behavior of two lasso peptides astexin-2 and astexin-3. Quantitative kinetics and energetics of the unthreading process were determined for variants of these peptides using a series of chromatography and mass spectrometry experiments and biased molecular dynamics (MD) simulations. In addition, we show that the Tyr15Phe variant of astexin-3 unthreads via an unprecedented "tail pulling" mechanism. MD simulations on a model ring-thread system coupled with machine learning approaches also led to the discovery of physicochemical descriptors most important for peptide unthreading.
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Affiliation(s)
- Caitlin D. Allen
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Maria Y. Chen
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Alexander Y. Trick
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Dan Thanh Le
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrew L. Ferguson
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - A. James Link
- Departments of Chemical and Biological Engineering and ‡Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Department of Materials
Science and Engineering and ∥Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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32
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Min D, Arbing MA, Jefferson RE, Bowie JU. A simple DNA handle attachment method for single molecule mechanical manipulation experiments. Protein Sci 2016; 25:1535-44. [PMID: 27222403 PMCID: PMC4972209 DOI: 10.1002/pro.2952] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
Manipulating single molecules and systems of molecules with mechanical force is a powerful technique to examine their physical properties. Applying force requires attachment of the target molecule to larger objects using some sort of molecular tether, such as a strand of DNA. DNA handle attachment often requires difficult manipulations of the target molecule, which can preclude attachment to unstable, hard to obtain, and/or large, complex targets. Here we describe a method for covalent DNA handle attachment to proteins that simply requires the addition of a preprepared reagent to the protein and a short incubation. The handle attachment method developed here provides a facile approach for studying the biomechanics of biological systems.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - Robert E Jefferson
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
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33
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Hoffmann T, Tych KM, Crosskey T, Schiffrin B, Brockwell DJ, Dougan L. Rapid and Robust Polyprotein Production Facilitates Single-Molecule Mechanical Characterization of β-Barrel Assembly Machinery Polypeptide Transport Associated Domains. ACS NANO 2015; 9:8811-21. [PMID: 26284289 DOI: 10.1021/acsnano.5b01962] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-molecule force spectroscopy by atomic force microscopy exploits the use of multimeric protein constructs, namely, polyproteins, to decrease the impact of nonspecific interactions, to improve data accumulation, and to allow the accommodation of benchmarking reference domains within the construct. However, methods to generate such constructs are either time- and labor-intensive or lack control over the length or the domain sequence of the obtained construct. Here, we describe an approach that addresses both of these shortcomings that uses Gibson assembly (GA) to generate a defined recombinant polyprotein rapidly using linker sequences. To demonstrate the feasibility of this approach, we used GA to make a polyprotein composed of alternating domains of I27 and TmCsp, (I27-TmCsp)3-I27)(GA), and showed the mechanical fingerprint, mechanical strength, and pulling speed dependence are the same as an analogous polyprotein constructed using the classical approach. After this benchmarking, we exploited this approach to facilitiate the mechanical characterization of POTRA domain 2 of BamA from E. coli (EcPOTRA2) by assembling the polyprotein (I27-EcPOTRA2)3-I27(GA). We show that, as predicted from the α + β topology, EcPOTRA2 domains are mechanically robust over a wide range of pulling speeds. Furthermore, we identify a clear correlation between mechanical robustness and brittleness for a range of other α + β proteins that contain the structural feature of proximal terminal β-strands in parallel geometry. We thus demonstrate that the GA approach is a powerful tool, as it circumvents the usual time- and labor-intensive polyprotein production process and allows for rapid production of new constructs for single-molecule studies. As shown for EcPOTRA2, this approach allows the exploration of the mechanical properties of a greater number of proteins and their variants. This improves our understanding of the relationship between structure and mechanical strength, increasing our ability to design proteins with tailored mechanical properties.
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Affiliation(s)
- Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Thomas Crosskey
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Bob Schiffrin
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, U.K
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34
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Lim NCH, Jackson SE. Molecular knots in biology and chemistry. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354101. [PMID: 26291690 DOI: 10.1088/0953-8984/27/35/354101] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules.
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Affiliation(s)
- Nicole C H Lim
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. Faculty of Sciences, Universiti Brunei Darussalam, Gadong BE 1410, Brunei Darussalam
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35
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Haglund E. Engineering covalent loops in proteins can serve as an on/off switch to regulate threaded topologies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354107. [PMID: 26291088 DOI: 10.1088/0953-8984/27/35/354107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Knots in proteins are under active investigation motivating refinements of current techniques and the development of tools to better understand the knotted topology. A strong focus is to identify new knots and expand upon the current understanding of their complex topology. Previous work has shown that the knotted topology, even in the simplest case of knots, encompasses a variety of unique challenges in folding and tying a chain. To bypass many of the in vitro experimental complications involved in working with knots, it is useful to apply methodologies to a more simplified system. The pierced lasso bundles (PLB), we discovered where a single disulphide bridge holds the threaded topology together, presents a simpler system to study knots in vitro. Having a disulphide bridge as an on/off switch between the threaded/unthreaded topology is advantageous because a covalent loop allows manipulation of the knot without directly altering affecting secondary and tertiary structure. Because disulphide bridges are commonly used in protein engineering, a pierced lasso (PL) topology can be easily introduced into a protein of interest to form a knotted topology within a given secondary structure. It is also important to take into account that if formed, disulphides can inadvertently introduce an unwanted PL. This was found upon determination of the crystal structure (PDB code 2YHG) of the recently de novo designed nucleoside hydrolase. Our detailed investigations of the PL presented here will allow researchers to look at the introduction of disulphide bridges in a larger context with respect to potential geometrical consequences on the structure and functional properties of proteins.
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Affiliation(s)
- Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California, San Diego (UCSD), La Jolla, CA 92093, USA. Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
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36
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Beedle AEM, Lezamiz A, Stirnemann G, Garcia-Manyes S. The mechanochemistry of copper reports on the directionality of unfolding in model cupredoxin proteins. Nat Commun 2015; 6:7894. [PMID: 26235284 PMCID: PMC4532836 DOI: 10.1038/ncomms8894] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/24/2015] [Indexed: 11/09/2022] Open
Abstract
Understanding the directionality and sequence of protein unfolding is crucial to elucidate the underlying folding free energy landscape. An extra layer of complexity is added in metalloproteins, where a metal cofactor participates in the correct, functional fold of the protein. However, the precise mechanisms by which organometallic interactions are dynamically broken and reformed on (un)folding are largely unknown. Here we use single molecule force spectroscopy AFM combined with protein engineering and MD simulations to study the individual unfolding pathways of the blue-copper proteins azurin and plastocyanin. Using the nanomechanical properties of the native copper centre as a structurally embedded molecular reporter, we demonstrate that both proteins unfold via two independent, competing pathways. Our results provide experimental evidence of a novel kinetic partitioning scenario whereby the protein can stochastically unfold through two distinct main transition states placed at the N and C termini that dictate the direction in which unfolding occurs.
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Affiliation(s)
- Amy E M Beedle
- Department of Physics, King's College London, London WC2R 2LS, UK
| | - Ainhoa Lezamiz
- Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
| | - Guillaume Stirnemann
- CNRS - Institut de Biologie Physico-Chimique - PSL Research University, Laboratoire de Biochimie Théorique, 75005 Paris, France
| | - Sergi Garcia-Manyes
- Department of Physics, King's College London, London WC2R 2LS, UK.,Randall Division of Cell and Molecular Biophysics, King's College London, London WC2R 2LS, UK
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37
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Crépin T, Swale C, Monod A, Garzoni F, Chaillet M, Berger I. Polyproteins in structural biology. Curr Opin Struct Biol 2015; 32:139-46. [PMID: 25996897 PMCID: PMC7125721 DOI: 10.1016/j.sbi.2015.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 04/23/2015] [Accepted: 04/27/2015] [Indexed: 12/21/2022]
Abstract
Structures have been determined for natural and recombinant polyproteins. Native HIV Gag polyprotein architecture was revealed by cryo-EM of immature capsids. Recombinant polyprotein technology has resolved sample preparation bottlenecks. The high-resolution structure of influenza polymerase has been solved. Single-molecule analysis of polyproteins revealed their folding characteristics.
Polyproteins are chains of covalently conjoined smaller proteins that occur in nature as versatile means to organize the proteome of viruses including HIV. During maturation, viral polyproteins are typically cleaved into the constituent proteins with different biological functions by highly specific proteases, and structural analyses at defined stages of this maturation process can provide clues for antiviral intervention strategies. Recombinant polyproteins that use similar mechanisms are emerging as powerful tools for producing hitherto inaccessible protein targets such as the influenza polymerase, for high-resolution structure determination by X-ray crystallography. Conversely, covalent linking of individual protein subunits into single polypeptide chains are exploited to overcome sample preparation bottlenecks. Moreover, synthetic polyproteins provide a promising tool to dissect dynamic folding of polypeptide chains into three-dimensional architectures in single-molecule structure analysis by atomic force microscopy (AFM). The recent use of natural and synthetic polyproteins in structural biology and major achievements are highlighted in this contribution.
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Affiliation(s)
- Thibaut Crépin
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France.
| | - Christopher Swale
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Alexandre Monod
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Frederic Garzoni
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; The European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France
| | - Maxime Chaillet
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; The European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France
| | - Imre Berger
- Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France; The European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France; The School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom.
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38
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Jamroz M, Niemyska W, Rawdon EJ, Stasiak A, Millett KC, Sułkowski P, Sulkowska JI. KnotProt: a database of proteins with knots and slipknots. Nucleic Acids Res 2014; 43:D306-14. [PMID: 25361973 PMCID: PMC4383900 DOI: 10.1093/nar/gku1059] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints.
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Affiliation(s)
- Michal Jamroz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Wanda Niemyska
- Institute of Mathematics, University of Silesia, Bankowa 14, 40-007 Katowice, Poland
| | - Eric J Rawdon
- Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
| | - Kenneth C Millett
- Department of Mathematics, University of California, Santa Barbara, CA 93106, USA
| | - Piotr Sułkowski
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland California Institute of Technology, Pasadena, CA 91125, USA
| | - Joanna I Sulkowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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39
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Kotamarthi HC, Narayan S, Ainavarapu SRK. Mechanical unfolding of ribose binding protein and its comparison with other periplasmic binding proteins. J Phys Chem B 2014; 118:11449-54. [PMID: 25216062 DOI: 10.1021/jp507463q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Folding and unfolding studies on large, multidomain proteins are still rare despite their high abundance in genomes of prokaryotes and eukaryotes. Here, we investigate the unfolding properties of a 271 residue, two-domain ribose binding protein (RBP) from the bacterial periplasm using single-molecule force spectroscopy. We observe that RBP predominately unfolds via a two-state pathway with an unfolding force of ∼80 pN and an unfolding contour length of ∼95 nm. Only a small population (∼15%) of RBP follows three-state pathways. The ligand binding neither increases the mechanical stability nor influences the unfolding flux of RBP through different pathways. The kinetic partitioning between two-state and three-state pathways, which has been reported earlier for other periplasmic proteins, is also observed in RBP, albeit to a lesser extent. These results provide important insights into the mechanical stability and unfolding processes of large two-domain proteins and highlight the contrasting features upon ligand binding. Protein structural topology diagrams are used to explain the differences in the mechanical unfolding behavior of RBP with other periplasmic binding proteins.
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Affiliation(s)
- Hema Chandra Kotamarthi
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
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40
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He C, Lamour G, Xiao A, Gsponer J, Li H. Mechanically Tightening a Protein Slipknot into a Trefoil Knot. J Am Chem Soc 2014; 136:11946-55. [DOI: 10.1021/ja503997h] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chengzhi He
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Guillaume Lamour
- Center
for High Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Adam Xiao
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Joerg Gsponer
- Center
for High Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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41
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Kotamarthi HC, Sharma R, Narayan S, Ray S, Ainavarapu SRK. Multiple Unfolding Pathways of Leucine Binding Protein (LBP) Probed by Single-Molecule Force Spectroscopy (SMFS). J Am Chem Soc 2013; 135:14768-74. [DOI: 10.1021/ja406238q] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hema Chandra Kotamarthi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Riddhi Sharma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Satya Narayan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sayoni Ray
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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42
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Abstract
Most proteins, in order to perform their biological function, have to fold to a compact native state. The increasing number of knotted and slipknotted proteins identified suggests that proteins are able to manoeuvre around topological barriers during folding. In the present article, we review the current progress in elucidating the knotting process in proteins. Although we concentrate on theoretical approaches, where a knotted topology can be unambiguously detected, comparison with experiments is also reviewed. Numerical simulations suggest that the folding process for small knotted proteins is composed of twisted loop formation and then threading by either slipknot geometries or flipping. As the size of the knotted proteins increases, particularly for more deeply threaded termini, the prevalence of traps in the free energy landscape also increases. Thus, in the case of longer knotted and slipknotted proteins, the folding mechanism is probably supported by chaperones. Overall, results imply that knotted proteins can be folded efficiently and survive evolutionary pressure in order to perform their biological functions.
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43
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Abstract
The forced mechanical unfolding of the knotted protein Human Carbonic Anhydrase (HCA) III is examined by steered, explicit-water molecular dynamics computer simulations. In agreement with previous indications from experiments and coarse-grained simulations, knot tightening by pulling near-terminal amino acids (4 and 267) leads to a much higher resistance to unfolding than for knot untying, where pulling amino acids 4 and 253 untangles the knot by threading the C-terminal end out of the knotting loop. In particular, the resistance during knot tightening is observed to diverge due to a tightly tied-up enzymatic core of the HCA if it is coordinated by the catalytically important zinc ion. The underlying structural pictures are presented and discussed.
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Affiliation(s)
- Joachim Dzubiella
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner Platz 1, 14109 Berlin, Germany
- Department of Physics, Humboldt-University Berlin, Newtonstr. 15, 12489 Berlin, Germany
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44
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Yu T, Lee OS, Schatz GC. Steered molecular dynamics studies of the potential of mean force for peptide amphiphile self-assembly into cylindrical nanofibers. J Phys Chem A 2013; 117:7453-60. [PMID: 23510255 DOI: 10.1021/jp401508w] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Steered molecular dynamics (SMD) simulations were applied to determine the potential of mean force for the self-assembly of peptide amphiphile (PA) nanofibers, specifically considering a single PA adding to a growing cylindrical nanofiber at 310 K. It is found that the free energy, enthalpy, and entropy differences for this assembly process are -67 kcal/mol, -71.5 kcal/ml, and -14.5 cal/(mol K), respectively, and therefore that enthalpy provides the driving force for self-assembly to form a fiber. A pairwise interaction analysis shows that both electrostatic and van der Waals interactions play important roles in the self-assembly process, with the van der Waals interaction being the larger effect. The mechanistic picture that emerges from this work is that as the PA is pulled from the fiber, the interaction evolves through three stages: (1) initially electrostatic interactions between the charged head of the pulled PA and other PAs, and between the pulled PA and solvent are dominant, (2) after the charged head emerges, the rest of the peptide comes out, with both PA-solvent electrostatic interactions and van der Waals interactions being significant, and (3) in the last step, the alkane tail emerges, dominated by van der Waals interactions with either peptide or solvent.
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Affiliation(s)
- Tao Yu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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45
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Sikora M, Cieplak M. Formation of cystine slipknots in dimeric proteins. PLoS One 2013; 8:e57443. [PMID: 23520470 PMCID: PMC3592873 DOI: 10.1371/journal.pone.0057443] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
We consider mechanical stability of dimeric and monomeric proteins with the cystine knot motif. A structure based dynamical model is used to demonstrate that all dimeric and some monomeric proteins of this kind should have considerable resistance to stretching that is significantly larger than that of titin. The mechanisms of the large mechanostability are elucidated. In most cases, it originates from the induced formation of one or two cystine slipknots. Since there are four termini in a dimer, there are several ways of selecting two of them to pull by. We show that in the cystine knot systems, there is strong anisotropy in mechanostability and force patterns related to the selection. We show that the thermodynamic stability of the dimers is enhanced compared to the constituting monomers whereas machanostability is either lower or higher.
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Affiliation(s)
- Mateusz Sikora
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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46
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Hoffmann T, Tych KM, Hughes ML, Brockwell DJ, Dougan L. Towards design principles for determining the mechanical stability of proteins. Phys Chem Chem Phys 2013; 15:15767-80. [DOI: 10.1039/c3cp52142g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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47
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Heidarsson PO, Naqvi MM, Sonar P, Valpapuram I, Cecconi C. Conformational Dynamics of Single Protein Molecules Studied by Direct Mechanical Manipulation. DYNAMICS OF PROTEINS AND NUCLEIC ACIDS 2013; 92:93-133. [DOI: 10.1016/b978-0-12-411636-8.00003-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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48
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Zoldák G, Rief M. Force as a single molecule probe of multidimensional protein energy landscapes. Curr Opin Struct Biol 2012; 23:48-57. [PMID: 23279960 DOI: 10.1016/j.sbi.2012.11.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/26/2012] [Accepted: 11/26/2012] [Indexed: 01/06/2023]
Abstract
Force spectroscopy has developed into an indispensable tool for studying folding and binding of proteins on a single molecule level in real time. Design of the pulling geometry allows tuning the reaction coordinate in a very precise manner. Many recent experiments have taken advantage of this possibility and have provided detailed insight the folding pathways on the complex high dimensional energy landscape. Beyond its potential to provide control over the reaction coordinate, force is also an important physiological parameter that affects protein conformation under in vivo conditions. Single molecule force spectroscopy studies have started to unravel the response and adaptation of force bearing protein structures to mechanical loads.
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Affiliation(s)
- Gabriel Zoldák
- Physik Department E22, Technische Universität München, James-Franck-Strasse, 85748 Garching, Germany
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49
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Using simulations to provide the framework for experimental protein folding studies. Arch Biochem Biophys 2012; 531:128-35. [PMID: 23266569 DOI: 10.1016/j.abb.2012.12.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 12/10/2012] [Accepted: 12/14/2012] [Indexed: 12/27/2022]
Abstract
Molecular dynamics simulations are a powerful theoretical tool to model the protein folding process in atomistic details under realistic conditions. Combined with a number of experimental techniques, simulations provide a detailed picture of how a protein folds or unfolds in the presence of explicit solvent and other molecular species, such as cosolvents, osmolytes, cofactors, active binding partners or inert crowding agents. The denaturing effects of temperature, pressure and external mechanical forces can also be probed. Qualitative and quantitative agreement with experiment contributes to a comprehensive molecular picture of protein states along the folding/unfolding pathway. The variety of systems examined reveals key features of the protein folding process.
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