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Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
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Yuan G, Curtolo F, Deng Y, Wu T, Tian F, Ma Q, Liu Y, Zuo J, Arantes GM, Zheng P. Highly Dynamic Polynuclear Metal Cluster Revealed in a Single Metallothionein Molecule. RESEARCH 2021; 2021:9756945. [PMID: 34368766 PMCID: PMC8299258 DOI: 10.34133/2021/9756945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/04/2021] [Indexed: 11/06/2022]
Abstract
Human metallothionein (MT) is a small-size yet efficient metal-binding protein, playing an essential role in metal homeostasis and heavy metal detoxification. MT contains two domains, each forming a polynuclear metal cluster with an exquisite hexatomic ring structure. The apoprotein is intrinsically disordered, which may strongly influence the clusters and the metal-thiolate (M-S) bonds, leading to a highly dynamic structure. However, these features are challenging to identify due to the transient nature of these species. The individual signal from dynamic conformations with different states of the cluster and M-S bond will be averaged and blurred in classic ensemble measurement. To circumvent these problems, we combined a single-molecule approach and multiscale molecular simulations to investigate the rupture mechanism and chemical stability of the metal cluster by a single MT molecule, focusing on the Zn4S11 cluster in the α domain upon unfolding. Unusual multiple unfolding pathways and intermediates are observed for both domains, corresponding to different combinations of M-S bond rupture. None of the pathways is clearly preferred suggesting that unfolding proceeds from the distribution of protein conformational substates with similar M-S bond strengths. Simulations indicate that the metal cluster may rearrange, forming and breaking metal-thiolate bonds even when MT is folded independently of large protein backbone reconfiguration. Thus, a highly dynamic polynuclear metal cluster with multiple conformational states is revealed in MT, responsible for the binding promiscuity and diverse cellular functions of this metal-carrier protein.
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Affiliation(s)
- Guodong Yuan
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Felipe Curtolo
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, 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, China
| | - Qun Ma
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yutong Liu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jinglin Zuo
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Guilherme Menegon Arantes
- Department of Biochemistry, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
| | - 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, China
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53
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Zhang S, Weng Y, Ma C. Quantitative Nanomechanical Mapping of Polyolefin Elastomer at Nanoscale with Atomic Force Microscopy. NANOSCALE RESEARCH LETTERS 2021; 16:113. [PMID: 34216298 PMCID: PMC8254710 DOI: 10.1186/s11671-021-03568-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Elastomeric nanostructures are normally expected to fulfill an explicit mechanical role and therefore their mechanical properties are pivotal to affect material performance. Their versatile applications demand a thorough understanding of the mechanical properties. In particular, the time dependent mechanical response of low-density polyolefin (LDPE) has not been fully elucidated. Here, utilizing state-of-the-art PeakForce quantitative nanomechanical mapping jointly with force volume and fast force volume, the elastic moduli of LDPE samples were assessed in a time-dependent fashion. Specifically, the acquisition frequency was discretely changed four orders of magnitude from 0.1 up to 2 k Hz. Force data were fitted with a linearized DMT contact mechanics model considering surface adhesion force. Increased Young's modulus was discovered with increasing acquisition frequency. It was measured 11.7 ± 5.2 MPa at 0.1 Hz and increased to 89.6 ± 17.3 MPa at 2 kHz. Moreover, creep compliance experiment showed that instantaneous elastic modulus E1, delayed elastic modulus E2, viscosity η, retardation time τ were 22.3 ± 3.5 MPa, 43.3 ± 4.8 MPa, 38.7 ± 5.6 MPa s and 0.89 ± 0.22 s, respectively. The multiparametric, multifunctional local probing of mechanical measurement along with exceptional high spatial resolution imaging open new opportunities for quantitative nanomechanical mapping of soft polymers, and can potentially be extended to biological systems.
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Affiliation(s)
- Shuting Zhang
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, Henan, China.
| | - Yihui Weng
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Chunhua Ma
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, Henan, China.
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A single residue deletion in the barley HKT1;5 P189 variant restores plasma membrane localisation but not Na + conductance. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183669. [PMID: 34139196 DOI: 10.1016/j.bbamem.2021.183669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
Leaf Na+ exclusion, mediated by plasma membrane-localised Class 1 High-affinity potassium (K+) Transporters (HKTs), is a key mechanism contributing to salinity tolerance of several major crop plants. We determined previously that the leucine to proline residue substitution at position 189 (L189P) in barley HvHKT1;5 disrupts its characteristic plasma membrane localisation and Na+ conductance. Here, we focus on a surprising observation that a single residue deletion of methionine at position 372 (M372del) within the conserved VMMYL motif in plant HKTs, restores plasma membrane localisation but not Na+ conductance in HvHKT1;5 P189. To clarify why the singular M372 deletion regains plasma membrane localisation, we built 3D models and defined α-helical assembly pathways of the P189 M372del mutant, and compared these findings to the wild-type protein, and the HvHKT1;5 L189 variant and its M372del mutant. We find that α-helical association and assembly pathways in HvHKT1;5 proteins fall in two contrasting categories. Inspections of structural flexibility through molecular dynamics simulations revealed that the conformational states of HvHKT1;5 P189 diverge from those of the L189 variant and M372del mutants. We propose that M372del in HvHKT1;5 P189 instigates structural rearrangements allowing routing to the plasma membrane, while the restoration of conductance would require further interventions. We integrate the microscopy, electrophysiology, and biocomputational data and discuss how a profound structural change in HvHKT1;5 P189 M372del impacts its α-helical protein association pathway and flexibility, and how these features underlie a delicate balance leading to restoring plasma membrane localisation but not Na+ conductance.
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55
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Li Q, Apostolidou D, Marszalek PE. Reconstruction of mechanical unfolding and refolding pathways of proteins with atomic force spectroscopy and computer simulations. Methods 2021; 197:39-53. [PMID: 34020035 DOI: 10.1016/j.ymeth.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 12/29/2022] Open
Abstract
Most proteins in proteomes are large, typically consist of more than one domain and are structurally complex. This often makes studying their mechanical unfolding pathways challenging. Proteins composed of tandem repeat domains are a subgroup of multi-domain proteins that, when stretched, display a saw-tooth pattern in their mechanical unfolding force extension profiles due to their repetitive structure. However, the assignment of force peaks to specific repeats undergoing mechanical unraveling is complicated because all repeats are similar and they interact with their neighbors and form a contiguous tertiary structure. Here, we describe in detail a combination of experimental and computational single-molecule force spectroscopy methods that proved useful for examining the mechanical unfolding and refolding pathways of ankyrin repeat proteins. Specifically, we explain and delineate the use of atomic force microscope-based single molecule force spectroscopy (SMFS) to record the mechanical unfolding behavior of ankyrin repeat proteins and capture their unusually strong refolding propensity that is responsible for generating impressive refolding force peaks. We also describe Coarse Grain Steered Molecular Dynamic (CG-SMD) simulations which complement the experimental observations and provide insights in understanding the unfolding and refolding of these proteins. In addition, we advocate the use of novel coiled-coils-based mechanical polypeptide probes which we developed to demonstrate the vectorial character of folding and refolding of these repeat proteins. The combination of AFM-based SMFS on native and CC-equipped proteins with CG-SMD simulations is powerful not only for ankyrin repeat polypeptides, but also for other repeat proteins and more generally to various multidomain, non-repetitive proteins with complex topologies.
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Affiliation(s)
- Qing Li
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, 27708 Durham, NC, United States.
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56
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Bian K, Gerber C, Heinrich AJ, Müller DJ, Scheuring S, Jiang Y. Scanning probe microscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00033-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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57
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Energy landscapes of fast-folding proteins pushing the limits of atomic force microscope (AFM) pulling. Proc Natl Acad Sci U S A 2021; 118:2102946118. [PMID: 33893176 DOI: 10.1073/pnas.2102946118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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58
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Devaux F, Li X, Sluysmans D, Maurizot V, Bakalis E, Zerbetto F, Huc I, Duwez AS. Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding. Chem 2021. [DOI: 10.1016/j.chempr.2021.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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59
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Song G, Tian F, Liu H, Li G, Zheng P. Pioglitazone Inhibits Metal Cluster Transfer of mitoNEET by Stabilizing the Labile Fe-N Bond Revealed at Single-Bond Level. J Phys Chem Lett 2021; 12:3860-3867. [PMID: 33856229 DOI: 10.1021/acs.jpclett.0c03852] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Outer mitochondrial membrane protein mitoNEET (mNT) is a target of the type 2 diabetes drug pioglitazone. It contains a labile Fe2S2(His)1(Cys)3 metal cluster with a single Fe-N(His87) coordinating bond and can transfer its cluster to acceptor proteins. Previous ensemble studies showed that pioglitazone's binding inhibited the transfer by stabilizing the cluster, and histidine 87 may be the key mediator. Here we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to study the unfolding process of mNT dimer in the absence and presence of pioglitazone, which can distinguish the binding effect for different regions of a protein. By developing a two-step strategy using different mNT monomers with respective purification tags, we solve the problem that the classic polyprotein formation disables the mNT to dimerize. As a result, a polyprotein including a stable, naturally noncovalently bound mNT homodimer is obtained, which is required for reliable AFM measurement and pioglitazone binding. Then, the dissociation rate (koff) of the metal cluster was measured, showing a 10-fold decrease upon pioglitazone binding, while the other parts decreased only 3-fold, verifying that pioglitazone mainly stabilizes the cluster. Moreover, when the Fe(III)-N(His87) bond was ruptured, this effect for the remaining Fe2S2(Cys)3 intermediate largely disappeared. Consequently, AFM results revealed that pioglitazone inhibited the metal cluster transfer of mNT by stabilizing the labile Fe(III)-N(His87) bond. In addition, an alternative method to build a natural, noncovalently bound protein dimer or complex for reliable single-molecule measurement was developed.
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Affiliation(s)
- Guobin 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
| | - 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
| | - Huaxing Liu
- 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
| | - Guoqiang Li
- 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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60
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Lysy M, Zhu F, Yates B, Labuda A. Robust and Efficient Parametric Spectral Density Estimation for High-Throughput Data. Technometrics 2021. [DOI: 10.1080/00401706.2021.1884134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Martin Lysy
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Feiyu Zhu
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
| | - Bryan Yates
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada
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61
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Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy. Proc Natl Acad Sci U S A 2021; 118:2020083118. [PMID: 33753487 DOI: 10.1073/pnas.2020083118] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Single amino acid mutations provide quantitative insight into the energetics that underlie the dynamics and folding of membrane proteins. Chemical denaturation is the most widely used assay and yields the change in unfolding free energy (ΔΔG). It has been applied to >80 different residues of bacteriorhodopsin (bR), a model membrane protein. However, such experiments have several key limitations: 1) a nonnative lipid environment, 2) a denatured state with significant secondary structure, 3) error introduced by extrapolation to zero denaturant, and 4) the requirement of globally reversible refolding. We overcame these limitations by reversibly unfolding local regions of an individual protein with mechanical force using an atomic-force-microscope assay optimized for 2 μs time resolution and 1 pN force stability. In this assay, bR was unfolded from its native bilayer into a well-defined, stretched state. To measure ΔΔG, we introduced two alanine point mutations into an 8-amino-acid region at the C-terminal end of bR's G helix. For each, we reversibly unfolded and refolded this region hundreds of times while the rest of the protein remained folded. Our single-molecule-derived ΔΔG for mutant L223A (-2.3 ± 0.6 kcal/mol) quantitatively agreed with past chemical denaturation results while our ΔΔG for mutant V217A was 2.2-fold larger (-2.4 ± 0.6 kcal/mol). We attribute the latter result, in part, to contact between Val217 and a natively bound squalene lipid, highlighting the contribution of membrane protein-lipid contacts not present in chemical denaturation assays. More generally, we established a platform for determining ΔΔG for a fully folded membrane protein embedded in its native bilayer.
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62
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Modulation of a protein-folding landscape revealed by AFM-based force spectroscopy notwithstanding instrumental limitations. Proc Natl Acad Sci U S A 2021; 118:2015728118. [PMID: 33723041 DOI: 10.1073/pnas.2015728118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Single-molecule force spectroscopy is a powerful tool for studying protein folding. Over the last decade, a key question has emerged: how are changes in intrinsic biomolecular dynamics altered by attachment to μm-scale force probes via flexible linkers? Here, we studied the folding/unfolding of α3D using atomic force microscopy (AFM)-based force spectroscopy. α3D offers an unusual opportunity as a prior single-molecule fluorescence resonance energy transfer (smFRET) study showed α3D's configurational diffusion constant within the context of Kramers theory varies with pH. The resulting pH dependence provides a test for AFM-based force spectroscopy's ability to track intrinsic changes in protein folding dynamics. Experimentally, however, α3D is challenging. It unfolds at low force (<15 pN) and exhibits fast-folding kinetics. We therefore used focused ion beam-modified cantilevers that combine exceptional force precision, stability, and temporal resolution to detect state occupancies as brief as 1 ms. Notably, equilibrium and nonequilibrium force spectroscopy data recapitulated the pH dependence measured using smFRET, despite differences in destabilization mechanism. We reconstructed a one-dimensional free-energy landscape from dynamic data via an inverse Weierstrass transform. At both neutral and low pH, the resulting constant-force landscapes showed minimal differences (∼0.2 to 0.5 k B T) in transition state height. These landscapes were essentially equal to the predicted entropic barrier and symmetric. In contrast, force-dependent rates showed that the distance to the unfolding transition state increased as pH decreased and thereby contributed to the accelerated kinetics at low pH. More broadly, this precise characterization of a fast-folding, mechanically labile protein enables future AFM-based studies of subtle transitions in mechanoresponsive proteins.
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63
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Vilhena JG, Ortega M, Uhlig MR, Garcia R, Pérez R. Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G. ACS Sens 2021; 6:553-564. [PMID: 33503368 DOI: 10.1021/acssensors.0c02241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.
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Affiliation(s)
- J. G. Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Manuel R. Uhlig
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Ricardo Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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64
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Nicolaus F, Metola A, Mermans D, Liljenström A, Krč A, Abdullahi SM, Zimmer M, Miller Iii TF, von Heijne G. Residue-by-residue analysis of cotranslational membrane protein integration in vivo. eLife 2021; 10:64302. [PMID: 33554862 PMCID: PMC7886326 DOI: 10.7554/elife.64302] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
We follow the cotranslational biosynthesis of three multispanning Escherichia coli inner membrane proteins in vivo using high-resolution force profile analysis. The force profiles show that the nascent chain is subjected to rapidly varying pulling forces during translation and reveal unexpected complexities in the membrane integration process. We find that an N-terminal cytoplasmic domain can fold in the ribosome exit tunnel before membrane integration starts, that charged residues and membrane-interacting segments such as re-entrant loops and surface helices flanking a transmembrane helix (TMH) can advance or delay membrane integration, and that point mutations in an upstream TMH can affect the pulling forces generated by downstream TMHs in a highly position-dependent manner, suggestive of residue-specific interactions between TMHs during the integration process. Our results support the 'sliding' model of translocon-mediated membrane protein integration, in which hydrophobic segments are continually exposed to the lipid bilayer during their passage through the SecYEG translocon.
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Affiliation(s)
- Felix Nicolaus
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ane Metola
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daphne Mermans
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Amanda Liljenström
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Ajda Krč
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Matthew Zimmer
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Thomas F Miller Iii
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, United States
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory Stockholm University, Solna, Sweden
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65
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Kotov V, Mlynek G, Vesper O, Pletzer M, Wald J, Teixeira‐Duarte CM, Celia H, Garcia‐Alai M, Nussberger S, Buchanan SK, Morais‐Cabral JH, Loew C, Djinovic‐Carugo K, Marlovits TC. In-depth interrogation of protein thermal unfolding data with MoltenProt. Protein Sci 2021; 30:201-217. [PMID: 33140490 PMCID: PMC7737771 DOI: 10.1002/pro.3986] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/06/2023]
Abstract
Protein stability is a key factor in successful structural and biochemical research. However, the approaches for systematic comparison of protein stability are limited by sample consumption or compatibility with sample buffer components. Here we describe how miniaturized measurement of intrinsic tryptophan fluorescence (NanoDSF assay) in combination with a simplified description of protein unfolding can be used to interrogate the stability of a protein sample. We demonstrate that improved protein stability measures, such as apparent Gibbs free energy of unfolding, rather than melting temperature Tm , should be used to rank the results of thermostability screens. The assay is compatible with protein samples of any composition, including protein complexes and membrane proteins. Our data analysis software, MoltenProt, provides an easy and robust way to perform characterization of multiple samples. Potential applications of MoltenProt and NanoDSF include buffer and construct optimization for X-ray crystallography and cryo-electron microscopy, screening for small-molecule binding partners and comparison of effects of point mutations.
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Affiliation(s)
- Vadim Kotov
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Georg Mlynek
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
| | - Oliver Vesper
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Marina Pletzer
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
| | - Jiri Wald
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
| | - Celso M. Teixeira‐Duarte
- Instituto de Investigação e Inovação em Saúde (i3S) and Instituto de Biologia Molecular e Celular (IBMC)Universidade do PortoPortoPortugal
| | - Herve Celia
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Maria Garcia‐Alai
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- European Molecular Biology Laboratory (EMBL)Hamburg UnitHamburgGermany
| | - Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular SystemsUniversity of StuttgartStuttgartGermany
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - João H. Morais‐Cabral
- Instituto de Investigação e Inovação em Saúde (i3S) and Instituto de Biologia Molecular e Celular (IBMC)Universidade do PortoPortoPortugal
| | - Christian Loew
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- European Molecular Biology Laboratory (EMBL)Hamburg UnitHamburgGermany
| | - Kristina Djinovic‐Carugo
- Department of Structural and Computational Biology, Max Perutz Labs ViennaUniversity of ViennaViennaAustria
- Department of Biochemistry, Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia
| | - Thomas C. Marlovits
- Centre for Structural Systems Biology (CSSB)HamburgGermany
- Institute for Structural and Systems BiologyUniversity Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- German Electron Synchrotron Centre (DESY)HamburgGermany
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66
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Ding Y, Apostolidou D, Marszalek P. Mechanical Stability of a Small, Highly-Luminescent Engineered Protein NanoLuc. Int J Mol Sci 2020; 22:E55. [PMID: 33374567 PMCID: PMC7801952 DOI: 10.3390/ijms22010055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 11/16/2022] Open
Abstract
NanoLuc is a bioluminescent protein recently engineered for applications in molecular imaging and cellular reporter assays. Compared to other bioluminescent proteins used for these applications, like Firefly Luciferase and Renilla Luciferase, it is ~150 times brighter, more thermally stable, and smaller. Yet, no information is known with regards to its mechanical properties, which could introduce a new set of applications for this unique protein, such as a novel biomaterial or as a substrate for protein activity/refolding assays. Here, we generated a synthetic NanoLuc derivative protein that consists of three connected NanoLuc proteins flanked by two human titin I91 domains on each side and present our mechanical studies at the single molecule level by performing Single Molecule Force Spectroscopy (SMFS) measurements. Our results show each NanoLuc repeat in the derivative behaves as a single domain protein, with a single unfolding event occurring on average when approximately 72 pN is applied to the protein. Additionally, we performed cyclic measurements, where the forces applied to a single protein were cyclically raised then lowered to allow the protein the opportunity to refold: we observed the protein was able to refold to its correct structure after mechanical denaturation only 16.9% of the time, while another 26.9% of the time there was evidence of protein misfolding to a potentially non-functional conformation. These results show that NanoLuc is a mechanically moderately weak protein that is unable to robustly refold itself correctly when stretch-denatured, which makes it an attractive model for future protein folding and misfolding studies.
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Affiliation(s)
- Yue Ding
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA; (Y.D.); (D.A.)
- Department of Engineering Mechanics, SVL, Xi’an Jiaotong University, Xi’an 710049, China
| | - Dimitra Apostolidou
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA; (Y.D.); (D.A.)
| | - Piotr Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA; (Y.D.); (D.A.)
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67
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Casuso I, Redondo-Morata L, Rico F. Biological physics by high-speed atomic force microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190604. [PMID: 33100165 PMCID: PMC7661283 DOI: 10.1098/rsta.2019.0604] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While many fields have contributed to biological physics, nanotechnology offers a new scale of observation. High-speed atomic force microscopy (HS-AFM) provides nanometre structural information and dynamics with subsecond resolution of biological systems. Moreover, HS-AFM allows us to measure piconewton forces within microseconds giving access to unexplored, fast biophysical processes. Thus, HS-AFM provides a tool to nourish biological physics through the observation of emergent physical phenomena in biological systems. In this review, we present an overview of the contribution of HS-AFM, both in imaging and force spectroscopy modes, to the field of biological physics. We focus on examples in which HS-AFM observations on membrane remodelling, molecular motors or the unfolding of proteins have stimulated the development of novel theories or the emergence of new concepts. We finally provide expected applications and developments of HS-AFM that we believe will continue contributing to our understanding of nature, by serving to the dialogue between biology and physics. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.
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Affiliation(s)
- Ignacio Casuso
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
| | - Lorena Redondo-Morata
- Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, 59000 Lille, France
| | - Felix Rico
- Aix-Marseile University, Inserm, CNRS, LAI, 163 Av. de Luminy, 13009 Marseille, France
- e-mail:
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68
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Yang B, Liu H, Liu Z, Doenen R, Nash MA. Influence of Fluorination on Single-Molecule Unfolding and Rupture Pathways of a Mechanostable Protein Adhesion Complex. NANO LETTERS 2020; 20:8940-8950. [PMID: 33191756 PMCID: PMC7729889 DOI: 10.1021/acs.nanolett.0c04178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/08/2020] [Indexed: 05/25/2023]
Abstract
We investigated the influence of fluorination on unfolding and unbinding reaction pathways of a mechanostable protein complex comprising the tandem dyad XModule-Dockerin bound to Cohesin. Using single-molecule atomic force spectroscopy, we mapped the energy landscapes governing the unfolding and unbinding reactions. We then used sense codon suppression to substitute trifluoroleucine in place of canonical leucine globally in XMod-Doc. Although TFL substitution thermally destabilized XMod-Doc, it had little effect on XMod-Doc:Coh binding affinity at equilibrium. When we mechanically dissociated global TFL-substituted XMod-Doc from Coh, we observed the emergence of a new unbinding pathway with a lower energy barrier. Counterintuitively, when fluorination was restricted to Doc, we observed mechano-stabilization of the non-fluorinated neighboring XMod domain. This suggests that intramolecular deformation is modulated by fluorination and highlights the differences between equilibrium thermostability and non-equilibrium mechanostability. Future work is poised to investigate fluorination as a means to modulate mechanical properties of synthetic proteins and hydrogels.
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Affiliation(s)
- Byeongseon Yang
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Regina Doenen
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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69
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Zhang P, Wang D, Yang W, Marszalek PE. Piecewise All-Atom SMD Simulations Reveal Key Secondary Structures in Luciferase Unfolding Pathway. Biophys J 2020; 119:2251-2261. [PMID: 33130123 DOI: 10.1016/j.bpj.2020.10.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/24/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023] Open
Abstract
Although the folding of single-domain proteins is well characterized theoretically and experimentally, the folding of large multidomain proteins is less well known. Firefly luciferase, a 550 residue three-domain protein, has been commonly used as a substrate to study chaperone reactions and as a model system for the study of folding of long polypeptide chains, including related phenomena such as cotranslational folding. Despite being characterized by various experimental techniques, the atomic-level contributions of various secondary structures of luciferase to its fold's mechanical stability remain unknown. Here, we developed a piecewise approach for all-atom steered molecular dynamics simulations to examine specific secondary structures that resist mechanical unfolding while minimizing the amount of computational resources required by the large water box of standard all-atom steered molecular dynamics simulations. We validated the robustness of this approach with a small NI3C protein and used our approach to elucidate the specific secondary structures that provide the largest contributions to luciferase mechanostability. In doing so, we show that piecewise all-atom steered molecular dynamics simulations can provide novel atomic resolution details regarding mechanostability and can serve as a platform for novel mutagenesis studies as well as a point for comparison with high-resolution force spectroscopy experiments.
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Affiliation(s)
- Pan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina
| | - David Wang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina.
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina.
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70
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Armstrong RE, Horáček M, Zijlstra P. Plasmonic Assemblies for Real-Time Single-Molecule Biosensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003934. [PMID: 33258287 DOI: 10.1002/smll.202003934] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/09/2020] [Indexed: 05/11/2023]
Abstract
Their tunable optical properties and versatile surface functionalization have sparked applications of plasmonic assemblies in the fields of biosensing, nonlinear optics, and photonics. Particularly, in the field of biosensing, rapid advances have occurred in the use of plasmonic assemblies for real-time single-molecule sensing. Compared to individual particles, the use of assemblies as sensors provides stronger signals, more control over the optical properties, and access to a broader range of timescales. In the past years, they have been used to directly reveal single-molecule interactions, mechanical properties, and conformational dynamics. This review summarizes the development of real-time single-molecule sensors built around plasmonic assemblies. First, a brief overview of their optical properties is given, and then recent applications are described. The current challenges in the field and suggestions to overcome those challenges are discussed in detail. Their stability, specificity, and sensitivity as sensors provide a complementary approach to other single-molecule techniques like force spectroscopy and single-molecule fluorescence. In future applications, the impact in real-time sensing on ultralong timescales (hours) and ultrashort timescales (sub-millisecond), time windows that are difficult to access using other techniques, is particularly foreseen.
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Affiliation(s)
- Rachel E Armstrong
- Department of Applied Physics & Institute for Complex Molecular Systems, Eindhoven University of Technology, Postbus 513, Eindhoven, MB, 5600, the Netherlands
| | - Matěj Horáček
- Department of Applied Physics & Institute for Complex Molecular Systems, Eindhoven University of Technology, Postbus 513, Eindhoven, MB, 5600, the Netherlands
| | - Peter Zijlstra
- Department of Applied Physics & Institute for Complex Molecular Systems, Eindhoven University of Technology, Postbus 513, Eindhoven, MB, 5600, the Netherlands
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71
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King GM, Kosztin I. Towards a Quantitative Understanding of Protein-Lipid Bilayer Interactions at the Single Molecule Level: Opportunities and Challenges. J Membr Biol 2020; 254:17-28. [PMID: 33196888 DOI: 10.1007/s00232-020-00151-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022]
Abstract
Protein-lipid interfaces are among the most fundamental in biology. Yet applying conventional techniques to study the biophysical attributes of these systems is challenging and has left many unknowns. For example, what is the kinetic pathway and energy landscape experienced by a polypeptide chain when in close proximity to a fluid lipid bilayer? Here we review the experimental and theoretical progress we have made in addressing this question from a single molecule perspective. Some remaining impediments are also discussed.
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Affiliation(s)
- Gavin M King
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA. .,Department of Biochemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA.
| | - Ioan Kosztin
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, 65211, USA.
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72
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Lv Y, Liang D, Lu S, Aurbach D, Xiang Y. Unidirectional electron injection and accelerated proton transport in bacteriorhodopsin based Bio-p-n junctions. Biosens Bioelectron 2020; 173:112811. [PMID: 33207301 DOI: 10.1016/j.bios.2020.112811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 11/21/2022]
Abstract
Hampered by the absence of evidence and theoretical model of biological semiconductors, the unidirectional electron transport via the p-n junction between functional proteins and abiotic materials remains a challenge for bioelectronics. Bacteriorhodopsin (bR), a representative transmembrane protein, has demonstrated exceptional optoelectronic effects in bR/semiconductor hybrid materials and offers a possible pathway for addressing this challenge. In the present work, for the first time, bR is proved to be an n-type semiconductor with an indirect electron transition. Through the photo-electrochemical method used for studying the p-n junction effect in the bR and p-type semiconductor combined electrodes, we reached several important conclusions: The self-corrosion of bR integrated Cu2O electrodes is delayed for about 36 times; The photocurrent of bR integrated CuSCN electrodes is enhanced by about 400%, which is attributed to the directional migration of electrons via the p-n junction. Furthermore, the ultrafast kinetics we have explored, shows that the injection of electrons shortens the lifetime of the intermediate state O640 from 37.3 μs to 20.1 μs, what means that the protons transport rate accompanying the bR photocycle process is accelerated. Therefore, we believe that the concept of the bio-p-n junction and the mechanism of electron coupled proton transport, which are discussed herein, will promote useful research on bioelectronic applications for bR and its homologs.
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Affiliation(s)
- Yujia Lv
- Department of Space and Environment, Beihang University, Beijing, 100191, PR China; Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, Beihang University, Beijing, 100191, PR China
| | - Dawei Liang
- Department of Space and Environment, Beihang University, Beijing, 100191, PR China
| | - Shanfu Lu
- Department of Space and Environment, Beihang University, Beijing, 100191, PR China; Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, Beihang University, Beijing, 100191, PR China
| | - Doron Aurbach
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yan Xiang
- Department of Space and Environment, Beihang University, Beijing, 100191, PR China; Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, Beihang University, Beijing, 100191, PR China; College of Engineering, Technology, and Aeronautics, Southern New Hampshire University, New Hampshire, 03106, USA.
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73
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Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D. Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chem Rev 2020; 121:11701-11725. [PMID: 33166471 DOI: 10.1021/acs.chemrev.0c00617] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.
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Affiliation(s)
- Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Hermann E Gaub
- Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 München, Germany
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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74
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Liu Z, Liu H, Vera AM, Bernardi RC, Tinnefeld P, Nash MA. High force catch bond mechanism of bacterial adhesion in the human gut. Nat Commun 2020; 11:4321. [PMID: 32859904 PMCID: PMC7456326 DOI: 10.1038/s41467-020-18063-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022] Open
Abstract
Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble substrates under hydrodynamic flow. Here we report the molecular mechanism behind an ultrastable protein complex responsible for resisting shear forces and adhering bacteria to cellulose fibers in the human gut. Using single-molecule force spectroscopy (SMFS), single-molecule FRET (smFRET), and molecular dynamics (MD) simulations, we resolve two binding modes and three unbinding reaction pathways of a mechanically ultrastable R. champanellensis (Rc) Dockerin:Cohesin (Doc:Coh) complex. The complex assembles in two discrete binding modes with significantly different mechanical properties, with one breaking at ~500 pN and the other at ~200 pN at loading rates from 1-100 nN s-1. A neighboring X-module domain allosterically regulates the binding interaction and inhibits one of the low-force pathways at high loading rates, giving rise to a catch bonding mechanism that manifests under force ramp protocols. Multi-state Monte Carlo simulations show strong agreement with experimental results, validating the proposed kinetic scheme. These results explain mechanistically how gut microbes regulate cell adhesion strength at high shear stress through intricate molecular mechanisms including dual-binding modes, mechanical allostery and catch bonds.
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Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801, Urbana, IL, USA
- Department of Physics, Auburn University, 36849, Auburn, AL, USA
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
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75
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Alunda BO, Lee YJ. Review: Cantilever-Based Sensors for High Speed Atomic Force Microscopy. SENSORS (BASEL, SWITZERLAND) 2020; 20:E4784. [PMID: 32854193 PMCID: PMC7506678 DOI: 10.3390/s20174784] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022]
Abstract
This review critically summarizes the recent advances of the microcantilever-based force sensors for atomic force microscope (AFM) applications. They are one the most common mechanical spring-mass systems and are extremely sensitive to changes in the resonant frequency, thus finding numerous applications especially for molecular sensing. Specifically, we comment on the latest progress in research on the deflection detection systems, fabrication, coating and functionalization of the microcantilevers and their application as bio- and chemical sensors. A trend on the recent breakthroughs on the study of biological samples using high-speed atomic force microscope is also reported in this review.
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Affiliation(s)
- Bernard Ouma Alunda
- School of Mines and Engineering, Taita Taveta University, P.O. Box 635-80300 Voi, Kenya;
| | - Yong Joong Lee
- School of Mechanical Engineering, Kyungpook National University, Daegu 41566, Korea
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76
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Marszalek PE, Oberhauser AF. Meeting report - NSF-sponsored workshop 'Progress and Prospects of Single-Molecule Force Spectroscopy in Biological and Chemical Sciences'. J Cell Sci 2020; 133:jcs251421. [PMID: 32817164 PMCID: PMC10679350 DOI: 10.1242/jcs.251421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
The goals of the workshop organized by Piotr Marszalek and Andres Oberhauser that took place between 29 August and 1 September 2019 at Duke University were to bring together leading experts and junior researchers to review past accomplishments, recent advances and limitations in the single-molecule force spectroscopy field, which examines nanomechanical forces in diverse biological processes and pathologies. Talks were organized into four sessions, and two in-depth roundtable discussion sessions were held.
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Affiliation(s)
- Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Andres F Oberhauser
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
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77
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Yu H, Jacobson DR, Luo H, Perkins TT. Quantifying the Native Energetics Stabilizing Bacteriorhodopsin by Single-Molecule Force Spectroscopy. PHYSICAL REVIEW LETTERS 2020; 125:068102. [PMID: 32845671 DOI: 10.1103/physrevlett.125.068102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
We quantified the equilibrium (un)folding free energy ΔG_{0} of an eight-amino-acid region starting from the fully folded state of the model membrane-protein bacteriorhodopsin using single-molecule force spectroscopy. Analysis of equilibrium and nonequilibrium data yielded consistent, high-precision determinations of ΔG_{0} via multiple techniques (force-dependent kinetics, Crooks fluctuation theorem, and inverse Boltzmann analysis). We also deduced the full 1D projection of the free-energy landscape in this region. Importantly, ΔG_{0} was determined in bacteriorhodopsin's native bilayer, an advance over traditional results obtained by chemical denaturation in nonphysiological detergent micelles.
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Affiliation(s)
- Hao Yu
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - David R Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
| | - Hao Luo
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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78
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Jacobson DR, Perkins TT. Correcting molecular transition rates measured by single-molecule force spectroscopy for limited temporal resolution. Phys Rev E 2020; 102:022402. [PMID: 32942397 DOI: 10.1103/physreve.102.022402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
Equilibrium free-energy-landscape parameters governing biomolecular folding can be determined from nonequilibrium force-induced unfolding by measuring the rates k for transitioning back and forth between states as a function of force F. However, bias in the observed forward and reverse rates is introduced by limited effective temporal resolution, which includes the mechanical response time of the force probe and any smoothing used to improve the signal-to-noise ratio. Here we use simulations to characterize this bias, which is most prevalent when the ratio of forward and reverse rates is far from unity. We find deviations in k(F) at high rates, due to unobserved transitions from short- to long-lived states, and at low rates, due to the corresponding unobserved transitions from long- to short-lived states. These missing events introduce erroneous curvature in log(k) vs F that leads to incorrect landscape parameter determination. To correct the measured k(F), we derive a pair of model-independent analytical formulas. The first correction accounts for unobserved transitions from short- to long-lived states, but does surprisingly little to correct the erroneous energy-landscape parameters. Only by subsequently applying the second formula, which corrects the corresponding reverse process, do we recover the expected k(F) and energy-landscape quantities. Going forward, these corrections should be applied to transition-rate data whenever the highest measured rate is not at least an order of magnitude slower than the effective temporal resolution.
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Affiliation(s)
- David R Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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79
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Sanchez-Guzman D, Giraudon-Colas G, Marichal L, Boulard Y, Wien F, Degrouard J, Baeza-Squiban A, Pin S, Renault JP, Devineau S. In Situ Analysis of Weakly Bound Proteins Reveals Molecular Basis of Soft Corona Formation. ACS NANO 2020; 14:9073-9088. [PMID: 32633939 DOI: 10.1021/acsnano.0c04165] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Few experimental techniques allow the analysis of the protein corona in situ. As a result, little is known on the effects of nanoparticles on weakly bound proteins that form the soft corona. Despite its biological importance, our understanding of the molecular bases driving its formation is limited. Here, we show that hemoglobin can form either a hard or a soft corona on silica nanoparticles depending on the pH conditions. Using cryoTEM and synchrotron-radiation circular dichroism, we show that nanoparticles alter the structure and the stability of weakly bound proteins in situ. Molecular dynamics simulation identified the structural elements driving protein-nanoparticle interaction. Based on thermodynamic analysis, we show that nanoparticles stabilize partially unfolded protein conformations by enthalpy-driven molecular interactions. We suggest that nanoparticles alter weakly bound proteins by shifting the equilibrium toward the unfolded states at physiological temperature. We show that the classical approach based on nanoparticle separation from the biological medium fails to detect destabilization of weakly bound proteins, and therefore cannot be used to fully predict the biological effects of nanomaterials in situ.
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Affiliation(s)
| | | | - Laurent Marichal
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay Cedex, France
| | - Yves Boulard
- Université Paris-Saclay, CEA, CNRS, I2BC, B3S, Gif-sur-Yvette 91190, France
| | - Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay Cedex, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, Gif-sur-Yvette 91190, France
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80
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Yang B, Liu Z, Liu H, Nash MA. Next Generation Methods for Single-Molecule Force Spectroscopy on Polyproteins and Receptor-Ligand Complexes. Front Mol Biosci 2020; 7:85. [PMID: 32509800 PMCID: PMC7248566 DOI: 10.3389/fmolb.2020.00085] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Single-molecule force spectroscopy with the atomic force microscope provides molecular level insights into protein function, allowing researchers to reconstruct energy landscapes and understand functional mechanisms in biology. With steadily advancing methods, this technique has greatly accelerated our understanding of force transduction, mechanical deformation, and mechanostability within single- and multi-domain polyproteins, and receptor-ligand complexes. In this focused review, we summarize the state of the art in terms of methodology and highlight recent methodological improvements for AFM-SMFS experiments, including developments in surface chemistry, considerations for protein engineering, as well as theory and algorithms for data analysis. We hope that by condensing and disseminating these methods, they can assist the community in improving data yield, reliability, and throughput and thereby enhance the information that researchers can extract from such experiments. These leading edge methods for AFM-SMFS will serve as a groundwork for researchers cognizant of its current limitations who seek to improve the technique in the future for in-depth studies of molecular biomechanics.
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Affiliation(s)
- Byeongseon Yang
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhaowei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Haipei Liu
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael A. Nash
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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81
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Lomize AL, Schnitzer KA, Pogozheva ID. TMPfold: A Web Tool for Predicting Stability of Transmembrane α-Helix Association. J Mol Biol 2020; 432:3388-3394. [DOI: 10.1016/j.jmb.2019.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/15/2022]
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82
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Choi HK, Min D, Kang H, Shon MJ, Rah SH, Kim HC, Jeong H, Choi HJ, Bowie JU, Yoon TY. Watching helical membrane proteins fold reveals a common N-to-C-terminal folding pathway. Science 2020; 366:1150-1156. [PMID: 31780561 DOI: 10.1126/science.aaw8208] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/30/2019] [Accepted: 11/05/2019] [Indexed: 02/03/2023]
Abstract
To understand membrane protein biogenesis, we need to explore folding within a bilayer context. Here, we describe a single-molecule force microscopy technique that monitors the folding of helical membrane proteins in vesicle and bicelle environments. After completely unfolding the protein at high force, we lower the force to initiate folding while transmembrane helices are aligned in a zigzag manner within the bilayer, thereby imposing minimal constraints on folding. We used the approach to characterize the folding pathways of the Escherichia coli rhomboid protease GlpG and the human β2-adrenergic receptor. Despite their evolutionary distance, both proteins fold in a strict N-to-C-terminal fashion, accruing structures in units of helical hairpins. These common features suggest that integral helical membrane proteins have evolved to maximize their fitness with cotranslational folding.
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Affiliation(s)
- Hyun-Kyu Choi
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.,Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Duyoung Min
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.,Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea
| | - Hyunook Kang
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Min Ju Shon
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.,Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Sang-Hyun Rah
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.,School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.,Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Hak Chan Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hawoong Jeong
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hee-Jung Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
| | - James U Bowie
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.
| | - Tae-Young Yoon
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea. .,Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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83
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Berezhkovskii AM, Makarov DE. From Nonequilibrium Single-Molecule Trajectories to Underlying Dynamics. J Phys Chem Lett 2020; 11:1682-1688. [PMID: 32017851 DOI: 10.1021/acs.jpclett.9b03705] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single-molecule observations of biomolecular dynamics and folding are commonly rationalized using the model of diffusive dynamics on a free-energy landscape, which is inferred via the Boltzmann inversion of the equilibrium distribution of the experimental observable. Can the same model be applied to high-resolution single-molecule trajectories of molecular machines that lack thermal equilibrium so that the Boltzmann inversion method is inapplicable? In this Letter, we discuss two approaches to reconstructing the underlying free-energy landscape in such nonequilibrium systems and explore the performance of this model in application to trajectories with complex underlying dynamics.
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Affiliation(s)
- Alexander M Berezhkovskii
- Mathematical and Statistical Computing Laboratory, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dmitrii E Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Oden Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
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84
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Matin TR, Utjesanovic M, Sigdel KP, Smith VF, Kosztin I, King GM. Characterizing the Locus of a Peripheral Membrane Protein-Lipid Bilayer Interaction Underlying Protein Export Activity in E. coli. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2143-2152. [PMID: 32011890 DOI: 10.1021/acs.langmuir.9b03606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Quantitative characterization of the strength of peripheral membrane protein-lipid bilayer interactions is fundamental in the understanding of many protein targeting pathways. SecA is a peripheral membrane protein that plays a central role in translocating precursor proteins across the inner membrane of E. coli. The membrane binding activity of the extreme N-terminus of SecA is critical for translocase function. Yet, the mechanical strength of the interaction and the kinetic pathways that this segment of SecA experiences when in proximity of an E. coli polar lipid bilayer has not been characterized. We directly measured the N-terminal SecA-lipid bilayer interaction using precision single molecule atomic force microscope (AFM)-based dynamic force spectroscopy. To provide conformational data inaccessible to AFM, we also performed all-atom molecular dynamics simulations and circular dichroism measurements. The N-terminal 10 amino acids of SecA have little secondary structure when bound to zwitterionic lipid head groups, but secondary structure, which rigidifies the lipid-bound protein segment, emerges when negatively charged lipids are present. Analysis of the single molecule protein-lipid dissociation data converged to a well-defined lipid-bound-state lifetime in the absence of force, τ0lipid = 0.9 s, which is well separated from and longer than the fundamental time scale of the secretion process, defined as the time required to translocate a single amino acid residue (∼50 ms). This value of τ0lipid is likely to represent a lower limit of the in vivo membrane-bound lifetime due to factors including the minimal system employed here.
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Affiliation(s)
- Tina R Matin
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Milica Utjesanovic
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Krishna P Sigdel
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Virginia F Smith
- Department of Chemistry, United States Naval Academy, Annapolis, Maryland 21402, United States
| | - Ioan Kosztin
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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85
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Freitas FC, Junio de Oliveira R. Extension-Dependent Drift Velocity and Diffusion (DrDiff) Directly Reconstructs the Folding Free Energy Landscape of Atomic Force Microscopy Experiments. J Phys Chem Lett 2020; 11:800-807. [PMID: 31928018 DOI: 10.1021/acs.jpclett.9b02146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Two equilibrium force microscopy trajectories [q(t)] of high-precision single-molecule spectroscopy assays were analyzed: the pulling of an HIV RNA hairpin and of a 3-aa sequence of the bacteriorhodopsin membrane protein. Both present hundreds of two-state folding transitions, and their free-energy [F(q)] landscapes were previously obtained by deconvolving time signals with the inverse Boltzmann and pfold methods. In this letter, the two F profiles were reconstructed directly from the measured time-series by the drift-diffusion (DrDiff) framework that characterized the effective conformational drift-velocity [v(q)] and diffusion [D(q)] coefficients. The two thermodynamic F profiles reconstructed with DrDiff directly from q(t) were in good agreement with those previously obtained from the deconvolved time signals. q(t) trajectories simulated with a two-dimensional framework in which the diffusion coefficient of the pulling setup (q coordinate) differed from the molecule (x coordinate) were also analyzed by DrDiff. The performance in reconstructing F was investigated in different conditions of diffusion anisotropy in the simulated time-series using Brownian dynamics. In addition, recently developed theories were used in order to evaluate the quality of the analysis performed in the experimental time series: the memory effects and the intrinsic biomolecular dynamic properties after connecting the probe to the molecule. With the 2-dimensional diffusive models and the additional analyses, it is proposed that the different physical regimes imposed by the stiffer probes of the two biomolecules will have an impact in the measured extension-dependent D and, thus, in the reconstruction of F by DrDiff. Stiffer AFM probes may reflect the molecular behavior more faithfully and reconstruction of F might be more successful. The reported quantities extracted directly from q(t) highlights the current state of the biomolecule characterization by force spectroscopy experiments: it is still challenging despite the recent advances, yet it is very promising.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , 38064-200 MG , Brazil
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação , Universidade Federal do Triângulo Mineiro , Uberaba , 38064-200 MG , Brazil
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86
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Azulay H, Lutaty A, Qvit N. Approach for comparing protein structures and origami models. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183132. [PMID: 31738904 DOI: 10.1016/j.bbamem.2019.183132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/05/2019] [Accepted: 10/28/2019] [Indexed: 11/20/2022]
Abstract
The research fields of proteins and origami have intersected in the study of folding and de-novo design of proteins. However, there is limited knowledge on the analogy between protein structures and origami models. We propose a general approach for comparing protein structures with origami models, and present a test case, comparing transmembrane β-barrel and α-helical barrel with the Yoshimura and Kresling origami models. While both shapes and structures may look similar, we demonstrated that the β-barrel and the α-helical barrel are in agreement only with the shape and structural characteristics of the Kresling model. Through the analogy, it is explained how the structural characteristic can help the β-barrel and α-helical barrel to adjust length and diameter in response to changes in the membrane structure. However, such conformations only apply to the α-helical barrel, and the β-barrel, in spite of resembles to the Kresling model, remains stiff due to hydrogen bonds between the β-strands. Thus, our analysis suggests that there are similar patterns between protein structures and origami models and that the proposed approach may provide important insight on the role that the structure of a protein fulfils, and on the preferred structural design of novel proteins with unique characteristics.
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Affiliation(s)
| | | | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, POB 1589, Safed, Israel.
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87
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Balacescu L, Schrader TE, Radulescu A, Zolnierczuk P, Holderer O, Pasini S, Fitter J, Stadler AM. Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions. Sci Rep 2020; 10:1570. [PMID: 32005832 PMCID: PMC6994677 DOI: 10.1038/s41598-020-57775-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/06/2020] [Indexed: 11/22/2022] Open
Abstract
Equilibrium dynamics of different folding intermediates and denatured states is strongly connected to the exploration of the conformational space on the nanosecond time scale and might have implications in understanding protein folding. For the first time, the same protein system apomyoglobin has been investigated using neutron spin-echo spectroscopy in different states: native-like, partially folded (molten globule) and completely unfolded, following two different unfolding paths: using acid or guanidinium chloride (GdmCl). While the internal dynamics of the native-like state can be understood using normal mode analysis based on high resolution structural information of myoglobin, for the unfolded and even for the molten globule states, models from polymer science are employed. The Zimm model accurately describes the slowly-relaxing, expanded GdmCl-denaturated state, ignoring the individuality of the different aminoacid side chain. The dynamics of the acid unfolded and molten globule state are similar in the framework of the Zimm model with internal friction, where the chains still interact and hinder each other: the first Zimm relaxation time is as large as the internal friction time. Transient formation of secondary structure elements in the acid unfolded and presence of α-helices in the molten globule state lead to internal friction to a similar extent.
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Affiliation(s)
- Livia Balacescu
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Germany
| | - Tobias E Schrader
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany.
| | - Aurel Radulescu
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany
| | - Piotr Zolnierczuk
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) Outstation at Spallation Neutron Source (SNS), Oak Ridge, TN, 37831, USA
| | - Olaf Holderer
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany
| | - Stefano Pasini
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748, Garching, Germany
| | - Jörg Fitter
- I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Germany
- Forschungszentrum Jülich GmbH, Institute for Complex Systems (ICS-5), 52425, Jülich, Germany
| | - Andreas M Stadler
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056, Aachen, Germany
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems (ICS-1), 52425, Jülich, Germany
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88
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Ritzmann N, Thoma J. Mechanical Unfolding and Refolding of Single Membrane Proteins by Atomic Force Microscopy. Methods Mol Biol 2020; 2127:359-372. [PMID: 32112333 DOI: 10.1007/978-1-0716-0373-4_23] [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] [Indexed: 06/10/2023]
Abstract
Atomic force microscopy (AFM)-based single-molecule force spectroscopy allows direct physical manipulation of single membrane proteins under near-physiological conditions. It can be applied to study mechanical properties and molecular interactions as well as unfolding and folding pathways of membrane proteins. Here, we describe the basic procedure to study membrane proteins by single-molecule force spectroscopy and discuss general requirements of the experimental setup as well as common pitfalls typically encountered when working with membrane proteins in AFM.
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Affiliation(s)
- Noah Ritzmann
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Basel, Switzerland
| | - Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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89
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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90
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Mora M, Stannard A, Garcia-Manyes S. The nanomechanics of individual proteins. Chem Soc Rev 2020; 49:6816-6832. [DOI: 10.1039/d0cs00426j] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This tutorial review provides an overview of the single protein force spectroscopy field, including the main techniques and the basic tools for analysing the data obtained from the single molecule experiments.
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Affiliation(s)
- Marc Mora
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Andrew Stannard
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
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91
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Nash MA. Zig Zag AFM Protocol Reveals New Intermediate Folding States of Bacteriorhodopsin. Biophys J 2019; 118:538-540. [PMID: 32023441 DOI: 10.1016/j.bpj.2019.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/12/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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92
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Jacobson DR, Uyetake L, Perkins TT. Membrane-Protein Unfolding Intermediates Detected with Enhanced Precision Using a Zigzag Force Ramp. Biophys J 2019; 118:667-675. [PMID: 31882249 DOI: 10.1016/j.bpj.2019.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/22/2019] [Accepted: 12/03/2019] [Indexed: 01/15/2023] Open
Abstract
Precise quantification of the energetics and interactions that stabilize membrane proteins in a lipid bilayer is a long-sought goal. Toward this end, atomic force microscopy has been used to unfold individual membrane proteins embedded in their native lipid bilayer, typically by retracting the cantilever at a constant velocity. Recently, unfolding intermediates separated by as few as two amino acids were detected using focused-ion-beam-modified ultrashort cantilevers. However, unambiguously discriminating between such closely spaced states remains challenging, in part because any individual unfolding trajectory only occupies a subset of the total number of intermediates. Moreover, structural assignment of these intermediates via worm-like-chain analysis is hindered by brief dwell times compounded with thermal and instrumental noise. To overcome these issues, we moved the cantilever in a sawtooth pattern of 6-12 nm, offset by 0.25-1 nm per cycle, generating a "zigzag" force ramp of alternating positive and negative loading rates. We applied this protocol to the model membrane protein bacteriorhodopsin (bR). In contrast to conventional studies that extract bR's photoactive retinal along with the first transmembrane helix, we unfolded bR in the presence of its retinal. To do so, we introduced a previously developed enzymatic-cleavage site between helices E and F and pulled from the top of the E helix using a site-specific, covalent attachment. The resulting zigzag unfolding trajectories occupied 40% more states per trajectory and occupied those states for longer times than traditional constant-velocity records. In total, we identified 31 intermediates during the unfolding of five helices of EF-cleaved bR. These included a previously reported, mechanically robust intermediate located between helices C and B that, with our enhanced resolution, is now shown to be two distinct states separated by three amino acids. Interestingly, another intermediate directly interacted with the retinal, an interaction confirmed by removing the retinal.
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Affiliation(s)
- David R Jacobson
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado; Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado.
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93
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Covino R, Woodside MT, Hummer G, Szabo A, Cossio P. Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. J Chem Phys 2019; 151:154115. [PMID: 31640370 DOI: 10.1063/1.5118362] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers and the total extension of the molecule plus apparatus is monitored as a function of time. In a typical unfolding experiment at constant force, the total extension jumps between two values that correspond to the folded and unfolded states of the molecule. For several biomolecular systems, the committor, which is the probability to fold starting from a given extension, has been used to extract the molecular activation barrier (a technique known as "committor inversion"). In this work, we study the influence of the force probe, which is much larger than the molecule being measured, on the activation barrier obtained by committor inversion. We use a two-dimensional framework in which the diffusion coefficient of the molecule and of the pulling device can differ. We systematically study the free energy profile along the total extension obtained from the committor by numerically solving the Onsager equation and using Brownian dynamics simulations. We analyze the dependence of the extracted barrier on the linker stiffness, molecular barrier height, and diffusion anisotropy and, thus, establish the range of validity of committor inversion. Along the way, we showcase the committor of 2-dimensional diffusive models and illustrate how it is affected by barrier asymmetry and diffusion anisotropy.
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Affiliation(s)
- Roberto Covino
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Attila Szabo
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Pilar Cossio
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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94
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High-speed force spectroscopy: microsecond force measurements using ultrashort cantilevers. Biophys Rev 2019; 11:689-699. [PMID: 31588961 PMCID: PMC6815269 DOI: 10.1007/s12551-019-00585-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/27/2019] [Indexed: 10/25/2022] Open
Abstract
Complete understanding of the role of mechanical forces in biological processes requires knowledge of the mechanical properties of individual proteins and living cells. Moreover, the dynamic response of biological systems at the nano- and microscales span over several orders of magnitude in time, from sub-microseconds to several minutes. Thus, access to force measurements over a wide range of length and time scales is required. High-speed atomic force microscopy (HS-AFM) using ultrashort cantilevers has emerged as a tool to study the dynamics of biomolecules and cells at video rates. The adaptation of HS-AFM to perform high-speed force spectroscopy (HS-FS) allows probing protein unfolding and receptor/ligand unbinding up to the velocity of molecular dynamics (MD) simulations with sub-microsecond time resolution. Moreover, application of HS-FS on living cells allows probing the viscoelastic response at short time scales providing deep understanding of cytoskeleton dynamics. In this mini-review, we assess the principles and recent developments and applications of HS-FS using ultrashort cantilevers to probe molecular and cellular mechanics.
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95
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Krainer G, Keller S, Schlierf M. Structural dynamics of membrane-protein folding from single-molecule FRET. Curr Opin Struct Biol 2019; 58:124-137. [DOI: 10.1016/j.sbi.2019.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
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96
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Wang H, Chen Y, Zhang W. A single-molecule atomic force microscopy study reveals the antiviral mechanism of tannin and its derivatives. NANOSCALE 2019; 11:16368-16376. [PMID: 31436278 DOI: 10.1039/c9nr05410c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antiviral agents work by stopping or intervening the virus replication. Virus replication is a fast and multi-step process while effective antiviral intervention requires agents to interact with the protein coat, genetic RNA/DNA or both during virus replication. Thus, quantifying these interactions at the molecular level, although it is quite challenging, is very important for an understanding of the underlying molecular mechanism of antiviral intervention. Here, at the single molecule level, we employ single molecule force spectroscopy (SMFS) in combination with AFM imaging and choose tobacco mosaic virus (TMV)/tannin as a model system of tubular virus to directly study how the inhibitor influences the interactions of RNA and coat protein. We illustrated the antiviral mechanism of tannin during the three main stages of TMV infection, i.e., before the entry of cells, the disassembly of genetic RNA and reassembly of genetic RNA, respectively. Our SMFS results show that tannin and its derivatives can stabilize the TMV complex by enhancing the interactions between RNA and coat protein via weak interactions, such as hydrogen bonding and hydrophobic interactions. In addition, the stabilization effect showed molecular weight dependence, i.e., for higher molecular weight tannin the stabilization occurs after genetic RNA gets partially disassembled from the protein coat, while the lower molecular weight tannin hydrolyte starts experiencing the stabilization effect before the RNA disassembly. Furthermore, the cycling stretching-relaxation experiments in the presence/absence of tannin proved that tannin can prevent the assembling of RNA and coat protein. In addition, the AFM imaging results demonstrate that tannin can cause the aggregation of TMV particles in a concentration-dependent manner; a higher concentration of tannin will cause more severe aggregations. These results deepen our understanding of the antiviral mechanism of tannin and its derivatives, which facilitate the rational design of efficient agents for antiviral therapy.
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Affiliation(s)
- Huijie Wang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China.
| | - Ying Chen
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China.
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, P. R. China.
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97
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Yuan G, Liu H, Ma Q, Li X, Nie J, Zuo J, Zheng P. Single-Molecule Force Spectroscopy Reveals that Iron-Ligand Bonds Modulate Proteins in Different Modes. J Phys Chem Lett 2019; 10:5428-5433. [PMID: 31433648 DOI: 10.1021/acs.jpclett.9b01573] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The iron-amino acid interactions Fe-O(Glu/Asp), Fe-N(His), and Fe-S(Cys) are the three major iron-ligand bonds in proteins. To compare their properties in proteins, we used atomic force microscopy (AFM)-based single-molecule force spectroscopy to investigate a superoxide reductase (Fe(III)-SOR) with all three types of bonds forming an Fe(His)4CysGlu center. We first found that Apo-SOR without bound iron showed multiple unfolding pathways only from the β-barrel core. Then, using Holo-SOR with a ferric ion, we found that a single Fe-O(Glu) bond can tightly connect the flexible N-terminal fragment to the β-barrel and stabilize the whole protein, showing a complete protein unfolding scenario, while the single Fe-N(His) bond was weak and unable to provide such a stabilization. Moreover, when multiple Fe-N bonds are present, a similar stabilization effect can be achieved. Our results showed that the iron-ligand bond modulates protein structure and stability in different modes at the single-bond level.
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Affiliation(s)
- Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Huaxing Liu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Qun Ma
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Jinglin Zuo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
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98
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Ma Z, Yang P, Zhang X, Jiang K, Song Y, Zhang W. Quantifying the Chain Folding in Polymer Single Crystals by Single-Molecule Force Spectroscopy. ACS Macro Lett 2019; 8:1194-1199. [PMID: 35619456 DOI: 10.1021/acsmacrolett.9b00607] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Chain folding is a motif of polymer crystallization, which is essential for determining the crystallization kinetics. However, the experimental quantification of the chain folding remains a challenge because of limited instrumental resolution. Here, we quantify chain folding in solution-grown single crystals by using atomic force microscopy (AFM)-based single-molecule force spectroscopy. The fingerprint spectrum of force-induced chain motion allows us to decipher the adjacent and nonadjacent re-entry folding with spatial resolution of subnanometers. The average fractions of adjacent re-entry folds ⟨f⟩ are in the range 91-95% for polycaprolactone, poly-l-lactic acid, and polyamide 66, which is higher than the values determined by other classical technologies. The established single-molecule method is applicable to a broad range of crystalline polymer systems with different chain conformations or compositions.
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Affiliation(s)
- Ziwen Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Peng Yang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Xiaoye Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Ke Jiang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Yu Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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99
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Wang Z, Jumper JM, Freed KF, Sosnick TR. On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations. Biophys J 2019; 117:1429-1441. [PMID: 31587831 DOI: 10.1016/j.bpj.2019.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 08/25/2019] [Accepted: 09/12/2019] [Indexed: 11/25/2022] Open
Abstract
Single-molecule force spectroscopy has proven extremely beneficial in elucidating folding pathways for membrane proteins. Here, we simulate these measurements, conducting hundreds of unfolding trajectories using our fast Upside algorithm for slow enough speeds to reproduce key experimental features that may be missed using all-atom methods. The speed also enables us to determine the logarithmic dependence of pulling velocities on the rupture levels to better compare to experimental values. For simulations of atomic force microscope measurements in which force is applied vertically to the C-terminus of bacteriorhodopsin, we reproduce the major experimental features including even the back-and-forth unfolding of single helical turns. When pulling laterally on GlpG to mimic the experiment, we observe quite different behavior depending on the stiffness of the spring. With a soft spring, as used in the experimental studies with magnetic tweezers, the force remains nearly constant after the initial unfolding event, and a few pathways and a high degree of cooperativity are observed in both the experiment and simulation. With a stiff spring, however, the force drops to near zero after each major unfolding event, and numerous intermediates are observed along a wide variety of pathways. Hence, the mode of force application significantly alters the perception of the folding landscape, including the number of intermediates and the degree of folding cooperativity, important issues that should be considered when designing experiments and interpreting unfolding data.
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Affiliation(s)
- Zongan Wang
- Department of Chemistry, James Franck Institute, The University of Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - John M Jumper
- Department of Chemistry, James Franck Institute, The University of Chicago, Chicago, Illinois; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Karl F Freed
- Department of Chemistry, James Franck Institute, The University of Chicago, Chicago, Illinois.
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois; Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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100
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Hoffer NQ, Woodside MT. Probing microscopic conformational dynamics in folding reactions by measuring transition paths. Curr Opin Chem Biol 2019; 53:68-74. [PMID: 31479831 DOI: 10.1016/j.cbpa.2019.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/08/2019] [Accepted: 07/20/2019] [Indexed: 12/20/2022]
Abstract
Transition paths comprise those parts of a folding trajectory where the molecule passes through the high-energy transition states separating folded and unfolded conformations. The transition states determine the folding kinetics and mechanism but are difficult to observe because of their brief duration. Single-molecule experiments have in recent years begun to characterize transition paths in folding reactions, allowing the microscopic conformational dynamics that occur as a molecule traverses the energy barriers to be probed directly. Here we review single-molecule fluorescence and force spectroscopy measurements of transition-path properties, including the time taken to traverse the paths, the local velocity along them, the path shapes, and the variability within these measurements reflecting differences between individual barrier crossings. We discuss how these measurements have been related to theories of folding as diffusion over an energy landscape to deduce properties such as the diffusion coefficient, and how they are being combined with simulations to obtain enhanced atomistic understanding of folding. The richly detailed information available from transition path measurements holds great promise for improved understanding of microscopic mechanisms in folding.
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Affiliation(s)
- Noel Q Hoffer
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada.
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