1
|
Synakewicz M, Eapen RS, Perez-Riba A, Rowling PJE, Bauer D, Weißl A, Fischer G, Hyvönen M, Rief M, Itzhaki LS, Stigler J. Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix. ACS NANO 2022. [PMID: 35258937 DOI: 10.1101/2021.03.27.437344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Tandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs), superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between partially folded and unfolded conformations. We rationalize the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the center toward both termini simultaneously. Most strikingly, we also directly observe the protein's superhelical tertiary structure in the force signal. Using protein engineering, crystallography, and single-molecule experiments, we show that the superhelical geometry can be altered by carefully placed amino acid substitutions, and we examine how these sequence changes affect intrinsic repeat stability and inter-repeat coupling. Our findings provide the means to dissect and modulate repeat-protein stability and dynamics, which will be essential for researchers to understand the function of natural repeat proteins and to exploit artificial repeats proteins in nanotechnology and biomedical applications.
Collapse
Affiliation(s)
- Marie Synakewicz
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Rohan S Eapen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Albert Perez-Riba
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Pamela J E Rowling
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Daniela Bauer
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Andreas Weißl
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Matthias Rief
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom†
| | - Johannes Stigler
- Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 München, Germany
| |
Collapse
|
2
|
Synakewicz M, Eapen RS, Perez-Riba A, Rowling PJE, Bauer D, Weißl A, Fischer G, Hyvönen M, Rief M, Itzhaki LS, Stigler J. Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix. ACS NANO 2022; 16:3895-3905. [PMID: 35258937 PMCID: PMC8944806 DOI: 10.1021/acsnano.1c09162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Tandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs), superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between partially folded and unfolded conformations. We rationalize the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the center toward both termini simultaneously. Most strikingly, we also directly observe the protein's superhelical tertiary structure in the force signal. Using protein engineering, crystallography, and single-molecule experiments, we show that the superhelical geometry can be altered by carefully placed amino acid substitutions, and we examine how these sequence changes affect intrinsic repeat stability and inter-repeat coupling. Our findings provide the means to dissect and modulate repeat-protein stability and dynamics, which will be essential for researchers to understand the function of natural repeat proteins and to exploit artificial repeats proteins in nanotechnology and biomedical applications.
Collapse
Affiliation(s)
- Marie Synakewicz
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Rohan S. Eapen
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Albert Perez-Riba
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Pamela J. E. Rowling
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Daniela Bauer
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Andreas Weißl
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Gerhard Fischer
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Marko Hyvönen
- Department
of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
| | - Matthias Rief
- Physik-Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Laura S. Itzhaki
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Johannes Stigler
- Gene
Center Munich, Ludwig-Maximilians-Universität
München, Feodor-Lynen-Straße 25, 81377 München, Germany
| |
Collapse
|
3
|
Smirnov MA, Tolmachev DA, Glova AD, Sokolova MP, Geydt PV, Lukasheva NV, Lyulin SV. Combined Use of Atomic Force Microscopy and Molecular Dynamics in the Study of Biopolymer Systems. POLYMER SCIENCE SERIES C 2021. [DOI: 10.1134/s1811238221020089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
4
|
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: 1.0] [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.
Collapse
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.
| |
Collapse
|
5
|
Motta S, Pandini A, Fornili A, Bonati L. Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks. J Chem Theory Comput 2021; 17:2080-2089. [PMID: 33780250 PMCID: PMC8047803 DOI: 10.1021/acs.jctc.0c01308] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Several experimental
studies indicated that large conformational
changes, including partial domain unfolding, have a role in the functional
mechanisms of the basic helix loop helix Per/ARNT/SIM (bHLH-PAS) transcription
factors. Recently, single-molecule atomic force microscopy (AFM) revealed
two distinct pathways for the mechanical unfolding of the ARNT PAS-B.
In this work we used steered molecular dynamics simulations to gain
new insights into this process at an atomistic level. To reconstruct
and classify pathways sampled in multiple simulations, we designed
an original approach based on the use of self-organizing maps (SOMs).
This led us to identify two types of unfolding pathways for the ARNT
PAS-B, which are in good agreement with the AFM findings. Analysis
of average forces mapped on the SOM revealed a stable conformation
of the PAS-B along one pathway, which represents a possible structural
model for the intermediate state detected by AFM. The approach here
proposed will facilitate the study of other signal transmission mechanisms
involving the folding/unfolding of PAS domains.
Collapse
Affiliation(s)
- Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| | - Alessandro Pandini
- Department of Computer Science, Brunel University London, Uxbridge UB8 3PH, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.,The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan 20126, Italy
| |
Collapse
|
6
|
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: 8] [Impact Index Per Article: 2.7] [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.
Collapse
|
7
|
Li Q, Scholl ZN, Marszalek PE. Unraveling the Mechanical Unfolding Pathways of a Multidomain Protein: Phosphoglycerate Kinase. Biophys J 2019; 115:46-58. [PMID: 29972811 DOI: 10.1016/j.bpj.2018.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/31/2018] [Accepted: 05/21/2018] [Indexed: 01/12/2023] Open
Abstract
Phosphoglycerate kinase (PGK) is a highly conserved enzyme that is crucial for glycolysis. PGK is a monomeric protein composed of two similar domains and has been the focus of many studies for investigating interdomain interactions within the native state and during folding. Previous studies used traditional biophysical methods (such as circular dichroism, tryptophan fluorescence, and NMR) to measure signals over a large ensemble of molecules, which made it difficult to observe transient changes in stability or structure during unfolding and refolding of single molecules. Here, we unfold single molecules of PGK using atomic force spectroscopy and steered molecular dynamic computer simulations to examine the conformational dynamics of PGK during its unfolding process. Our results show that after the initial forced separation of its domains, yeast PGK (yPGK) does not follow a single mechanical unfolding pathway; instead, it stochastically follows two distinct pathways: unfolding from the N-terminal domain or unfolding from the C-terminal domain. The truncated yPGK N-terminal domain unfolds via a transient intermediate, whereas the structurally similar isolated C-terminal domain has no detectable intermediates throughout its mechanical unfolding process. The N-terminal domain in the full-length yPGK displays a strong unfolding intermediate 13% of the time, whereas the truncated domain (yPGKNT) transitions through the intermediate 81% of the time. This effect indicates that the mechanical properties of yPGK cannot be simply deduced from the mechanical properties of its constituents. We also find that Escherichia coli PGK is significantly less mechanically stable as compared to yPGK, contrary to bulk unfolding measurements. Our results support the growing body of observations that the folding behavior of multidomain proteins is difficult to predict based solely on the studies of isolated domains.
Collapse
Affiliation(s)
- Qing Li
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| | - Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| | - Piotr E Marszalek
- Center for Biologically Inspired Materials and Material Systems, Department of Mechanical Engineering and Materials Science, Pratt School of Engineering, Duke University, Durham, North Carolina.
| |
Collapse
|
8
|
Notari L, Martínez-Carranza M, Farías-Rico JA, Stenmark P, von Heijne G. Cotranslational Folding of a Pentarepeat β-Helix Protein. J Mol Biol 2018; 430:5196-5206. [PMID: 30539762 DOI: 10.1016/j.jmb.2018.10.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 02/07/2023]
Abstract
It is becoming increasingly clear that many proteins start to fold cotranslationally before the entire polypeptide chain has been synthesized on the ribosome. One class of proteins that a priori would seem particularly prone to cotranslational folding is repeat proteins, that is, proteins that are built from an array of nearly identical sequence repeats. However, while the folding of repeat proteins has been studied extensively in vitro with purified proteins, only a handful of studies have addressed the issue of cotranslational folding of repeat proteins. Here, we have determined the structure and studied the cotranslational folding of a β-helix pentarepeat protein from the human pathogen Clostridium botulinum-a homolog of the fluoroquinolone resistance protein MfpA-using an assay in which the SecM translational arrest peptide serves as a force sensor to detect folding events. We find that cotranslational folding of a segment corresponding to the first four of the eight β-helix coils in the protein produces enough force to release ribosome stalling and that folding starts when this unit is ~35 residues away from the P-site, near the distal end of the ribosome exit tunnel. An additional folding transition is seen when the whole PENT moiety emerges from the exit tunnel. The early cotranslational formation of a folded unit may be important to avoid misfolding events in vivo and may reflect the minimal size of a stable β-helix since it is structurally homologous to the smallest known β-helix protein, a four-coil protein that is stable in solution.
Collapse
Affiliation(s)
- Luigi Notari
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | | | | | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden.
| |
Collapse
|
9
|
|
10
|
Sing MK, Ramírez J, Olsen BD. Mechanical response of transient telechelic networks with many-part stickers. J Chem Phys 2017; 147:194902. [PMID: 29166120 DOI: 10.1063/1.4993649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A central question in soft matter is understanding how several individual, weak bonds act together to produce collective interactions. Here, gel-forming telechelic polymers with multiple stickers at each chain end are studied through Brownian dynamics simulations to understand how collective interaction of the bonds affects mechanical response of the gels. These polymers are modeled as finitely extensible dumbbells using an explicit tau-leap algorithm and the binding energy of these associations was kept constant regardless of the number of stickers. The addition of multiple bonds to the associating ends of telechelic polymers increases or decreases the network relaxation time depending on the relative kinetics of association but increases both shear stress and extensional viscosity. The relationship between the rate of association and the Rouse time of dangling chains results in two different regimes for the equilibrium stress relaxation of associating physical networks. In case I, a dissociated dangling chain is able to fully relax before re-associating to the network, resulting in two characteristic relaxation times and a non-monotonic terminal relaxation time with increasing number of bonds per polymer endgroup. In case II, the dissociated dangling chain is only able to relax a fraction of the way before it re-attaches to the network, and increasing the number of bonds per endgroup monotonically increases the terminal relaxation time. In flow, increasing the number of stickers increases the steady-state shear and extensional viscosities even though the overall bond kinetics and equilibrium constant remain unchanged. Increased dissipation in the simulations is primarily due to higher average chain extension with increasing bond number. These results indicate that toughness and dissipation in physically associating networks can both be increased by breaking single, strong bonds into smaller components.
Collapse
Affiliation(s)
- Michelle K Sing
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jorge Ramírez
- Departamento de Ingeniería Química Industrial Y Medio Ambiente, Universidad Politécnica de Madrid, Madrid 28006, Spain
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
11
|
Edwards DT, Perkins TT. Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution. J Struct Biol 2017; 197:13-25. [DOI: 10.1016/j.jsb.2016.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/13/2016] [Accepted: 01/18/2016] [Indexed: 11/24/2022]
|
12
|
Scholl ZN, Li Q, Yang W, Marszalek PE. Single-molecule Force Spectroscopy Reveals the Calcium Dependence of the Alternative Conformations in the Native State of a βγ-Crystallin Protein. J Biol Chem 2016; 291:18263-75. [PMID: 27378818 DOI: 10.1074/jbc.m116.729525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Indexed: 12/30/2022] Open
Abstract
Although multidomain proteins predominate the proteome of all organisms and are expected to display complex folding behaviors and significantly greater structural dynamics as compared with single-domain proteins, their conformational heterogeneity and its impact on their interaction with ligands are poorly understood due to a lack of experimental techniques. The multidomain calcium-binding βγ-crystallin proteins are particularly important because their deterioration and misfolding/aggregation are associated with melanoma tumors and cataracts. Here we investigate the mechanical stability and conformational dynamics of a model calcium-binding βγ-crystallin protein, Protein S, and elaborate on its interactions with calcium. We ask whether domain interactions and calcium binding affect Protein S folding and potential structural heterogeneity. Our results from single-molecule force spectroscopy show that the N-terminal (but not the C-terminal) domain is in equilibrium with an alternative conformation in the absence of Ca(2+), which is mechanically stable in contrast to other proteins that were observed to sample a molten globule under similar conditions. Mutagenesis experiments and computer simulations reveal that the alternative conformation of the N-terminal domain is caused by structural instability produced by the high charge density of a calcium binding site. We find that this alternative conformation in the N-terminal domain is diminished in the presence of calcium and can also be partially eliminated with a hitherto unrecognized compensatory mechanism that uses the interaction of the C-terminal domain to neutralize the electronegative site. We find that up to 1% of all identified multidomain calcium-binding proteins contain a similarly highly charged site and therefore may exploit a similar compensatory mechanism to prevent structural instability in the absence of ligand.
Collapse
Affiliation(s)
| | - Qing Li
- the Department of Mechanical Engineering and Materials Science, and
| | - Weitao Yang
- the Department of Chemistry, Duke University, Durham, North Carolina 27708
| | | |
Collapse
|
13
|
Direct Observation of the Reversible Two-State Unfolding and Refolding of an α/β Protein by Single-Molecule Atomic Force Microscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
14
|
He C, Hu C, Hu X, Hu X, Xiao A, Perkins TT, Li H. Direct Observation of the Reversible Two‐State Unfolding and Refolding of an α/β Protein by Single‐Molecule Atomic Force Microscopy. Angew Chem Int Ed Engl 2015; 54:9921-5. [DOI: 10.1002/anie.201502938] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/06/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Chengzhi He
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 (Canada)
| | - Chunguang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072 (China)
| | - Xiaodong Hu
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072 (China)
| | - Xiaotang Hu
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072 (China)
| | - Adam Xiao
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 (Canada)
| | - Thomas T. Perkins
- JILA, NIST and University of Colorado Boulder, Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, 440 UCB Boulder, CO 80309 (USA)
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 (Canada)
- State Key Laboratory of Precision Measurements Technology and Instruments, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, 300072 (China)
| |
Collapse
|
15
|
Bonilla LL, Carpio A, Prados A. Theory of force-extension curves for modular proteins and DNA hairpins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052712. [PMID: 26066204 DOI: 10.1103/physreve.91.052712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Indexed: 06/04/2023]
Abstract
We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by the elongations of each of the units. The system free energy includes a double-well potential for each unit and an elastic nearest-neighbor interaction between them. Minimizing the free energy yields the system equilibrium properties whereas its dynamics is given by (overdamped) Langevin equations for the elongations, in which friction and noise amplitude are related by the fluctuation-dissipation theorem. Our results, both for the equilibrium and the dynamical situations, include analytical and numerical descriptions of the system force-extension curves under force or length control and agree very well with actual experiments in biomolecules. Our conclusions also apply to other physical systems comprising a number of metastable units, such as storage systems or semiconductor superlattices.
Collapse
Affiliation(s)
- L L Bonilla
- G. Millán Institute, Fluid Dynamics, Nanoscience and Industrial Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - A Carpio
- Departamento de Matemática Aplicada, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - A Prados
- Física Teórica, Universidad de Sevilla, Apartado de Correos 1065, E-41080, Sevilla, Spain
| |
Collapse
|
16
|
Scholl ZN, Yang W, Marszalek PE. Direct observation of multimer stabilization in the mechanical unfolding pathway of a protein undergoing oligomerization. ACS NANO 2015; 9:1189-97. [PMID: 25639698 DOI: 10.1021/nn504686f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Understanding how protein oligomerization affects the stability of monomers in self-assembled structures is crucial to the development of new protein-based nanomaterials and protein cages for drug delivery. Here, we use single-molecule force spectroscopy (AFM-SMFS), protein engineering, and computer simulations to evaluate how dimerization and tetramerization affects the stability of the monomer of Streptavidin, a model homotetrameric protein. The unfolding force directly relates to the folding stability, and we find that monomer of Streptavidin is mechanically stabilized by 40% upon dimerization, and that it is stabilized an additional 24% upon tetramerization. We also find that biotin binding increases stability by another 50% as compared to the apo-tetrameric form. We used the distribution of unfolding forces to extract properties of the underlying energy landscape and found that the distance to the transition state is decreased and the barrier height is increased upon multimerization. Finally, we investigated the origin of the strengthening by ligand binding. We found that, rather than being strengthened through intramolecular contacts, it is strengthened due to the contacts provided by the biotin-binding loop that crosses the interface between the dimers.
Collapse
Affiliation(s)
- Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Duke University , Durham, North Carolina 27708, United States
| | | | | |
Collapse
|
17
|
Li Q, Scholl ZN, Marszalek PE. Capturing the Mechanical Unfolding Pathway of a Large Protein with Coiled-Coil Probes. Angew Chem Int Ed Engl 2014; 53:13429-33. [DOI: 10.1002/anie.201407211] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/10/2014] [Indexed: 11/08/2022]
|
18
|
Li Q, Scholl ZN, Marszalek PE. Capturing the Mechanical Unfolding Pathway of a Large Protein with Coiled-Coil Probes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
19
|
Scholl ZN, Yang W, Marszalek PE. Chaperones rescue luciferase folding by separating its domains. J Biol Chem 2014; 289:28607-18. [PMID: 25160632 DOI: 10.1074/jbc.m114.582049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Over the last 50 years, significant progress has been made toward understanding how small single-domain proteins fold. However, very little is known about folding mechanisms of medium and large multidomain proteins that predominate the proteomes of all forms of life. Large proteins frequently fold cotranslationally and/or require chaperones. Firefly (Photinus pyralis) luciferase (Luciferase, 550 residues) has been a model of a cotranslationally folding protein whose extremely slow refolding (approximately days) is catalyzed by chaperones. However, the mechanism by which Luciferase misfolds and how chaperones assist Luciferase refolding remains unknown. Here we combine single-molecule force spectroscopy (atomic force microscopy (AFM)/single-molecule force spectroscopy) with steered molecular dynamic computer simulations to unravel the mechanism of chaperone-assisted Luciferase refolding. Our AFM and steered molecular dynamic results show that partially unfolded Luciferase, with the N-terminal domain remaining folded, can refold robustly without chaperones. Complete unfolding causes Luciferase to get trapped in very stable non-native configurations involving interactions between N- and C-terminal residues. However, chaperones allow the completely unfolded Luciferase to refold quickly in AFM experiments, strongly suggesting that chaperones are able to sequester non-natively contacting residues. More generally, we suggest that many chaperones, rather than actively promoting the folding, mimic the ribosomal exit tunnel and physically separate protein domains, allowing them to fold in a cotranslational-like sequential process.
Collapse
Affiliation(s)
| | - Weitao Yang
- From the Program in Computational Biology and Bioinformatics, Department of Chemistry, and
| | - Piotr E Marszalek
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems, Duke University, Durham, North Carolina 27705
| |
Collapse
|
20
|
Scholl ZN, Li Q, Marszalek PE. Single molecule mechanical manipulation for studying biological properties of proteins,
DNA
, and sugars. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 6:211-29. [DOI: 10.1002/wnan.1253] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/10/2013] [Accepted: 10/17/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Zackary N. Scholl
- Department of Computational Biology and Bioinformatics Duke University Durham NC USA
| | - Qing Li
- Department of Mechanical Engineering and Materials Science Duke University Durham NC USA
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Center for Biologically Inspired Materials and Material Systems Duke University Durham NC USA
| |
Collapse
|
21
|
Sequential unfolding of beta helical protein by single-molecule atomic force microscopy. PLoS One 2013; 8:e73572. [PMID: 24009757 PMCID: PMC3756990 DOI: 10.1371/journal.pone.0073572] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 07/25/2013] [Indexed: 12/14/2022] Open
Abstract
The parallel βhelix is a common fold among extracellular proteins, however its mechanical properties remain unexplored. In Gram-negative bacteria, extracellular proteins of diverse functions of the large ‘TpsA’ family all fold into long βhelices. Here, single-molecule atomic force microscopy and steered molecular dynamics simulations were combined to investigate the mechanical properties of a prototypic TpsA protein, FHA, the major adhesin of Bordetella pertussis. Strong extension forces were required to fully unfold this highly repetitive protein, and unfolding occurred along a stepwise, hierarchical process. Our analyses showed that the extremities of the βhelix unfold early, while central regions of the helix are more resistant to mechanical unfolding. In particular, a mechanically resistant subdomain conserved among TpsA proteins and critical for secretion was identified. This nucleus harbors structural elements packed against the βhelix that might contribute to stabilizing the N-terminal region of FHA. Hierarchical unfolding of the βhelix in response to a mechanical stress may maintain β-helical portions that can serve as templates for regaining the native structure after stress. The mechanical properties uncovered here might apply to many proteins with β-helical or related folds, both in prokaryotes and in eukaryotes, and play key roles in their structural integrity and functions.
Collapse
|
22
|
Scholl ZN, Marszalek PE. Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions. Ultramicroscopy 2013; 136:7-14. [PMID: 24001740 DOI: 10.1016/j.ultramic.2013.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 07/17/2013] [Accepted: 07/25/2013] [Indexed: 12/30/2022]
Abstract
The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age.
Collapse
Affiliation(s)
- Zackary N Scholl
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.
| | | |
Collapse
|
23
|
Bujalowski PJ, Oberhauser AF. Tracking unfolding and refolding reactions of single proteins using atomic force microscopy methods. Methods 2013; 60:151-60. [PMID: 23523554 DOI: 10.1016/j.ymeth.2013.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 11/26/2022] Open
Abstract
During the last two decades single-molecule manipulation techniques such as atomic force microscopy (AFM) has risen to prominence through their unique capacity to provide fundamental information on the structure and function of biomolecules. Here we describe the use of single-molecule AFM to track protein unfolding and refolding pathways, enzymatic catalysis and the effects of osmolytes and chaperones on protein stability and folding. We will outline the principles of operation for two different AFM pulling techniques: length clamp and force-clamp and discuss prominent applications. We provide protocols for the construction of polyproteins which are amenable for AFM experiments, the preparation of different coverslips, choice and calibration of AFM cantilevers. We also discuss the selection criteria for AFM recordings, the calibration of AFM cantilevers, protein sample preparations and analysis of the obtained data.
Collapse
Affiliation(s)
- Paul J Bujalowski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, TX 77555, USA
| | | |
Collapse
|
24
|
|
25
|
Chen C, Wang E, Liu P, Xiao Y. Simulation study of the role of the ribosomal exit tunnel on protein folding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:022701. [PMID: 23496542 DOI: 10.1103/physreve.87.022701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 01/14/2013] [Indexed: 06/01/2023]
Abstract
To investigate the role of the ribosomal exit tunnel on protein folding, we simulate the initial-stage folding behavior of the protein villin headpiece subdomain HP35 (PDB id: 1yrf) with and without prefolding in the exit tunnel by using an all-atom model and find that prefolding in the exit tunnel could effectively help the protein form native secondary structures. Furthermore, our results show that, after releasing from the exit tunnel, the prefolded chains may have a tendency to form more native contacts than those only in free space and this reduces the conformational space of sampling. Our results may provide an alternative way to explain the fast folding mechanism of proteins in vivo.
Collapse
Affiliation(s)
- Changjun Chen
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | | | | | | |
Collapse
|
26
|
Settanni G, Serquera D, Marszalek PE, Paci E, Itzhaki LS. Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin. PLoS Comput Biol 2013; 9:e1002864. [PMID: 23341763 PMCID: PMC3547791 DOI: 10.1371/journal.pcbi.1002864] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 11/11/2012] [Indexed: 11/30/2022] Open
Abstract
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all aspects of the protein's mechanical behavior, including the order of repeat unfolding, the diversity of unfolding pathways accessed, the nature of partially unfolded intermediates, the forces required and the work transferred to the system to unfold the whole protein and its parts. Stepwise unfolding thus provides the means to buffer repeat proteins and their binding partners from mechanical stress in the cell. Our results illustrate how ligand binding can control the mechanical response of proteins. The data also point to a cellular mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress. Here we use molecular dynamics simulation to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with binding partner S6-C. Tandem repeat proteins like Gankyrin comprise tandem arrays of small structural motifs that pack linearly to produce elongated architectures. They are elastic, mechanically weak molecules and they unfold and refold repeat by repeat under force. We show that S6-C binding greatly increases the resistance of Gankyrin to mechanical stress. The enhanced mechanical stability is specific to those ankyrin repeats in contact with S6-C, and the localized nature of the effect results in fundamental changes in the way the protein responds to force. Thus, the forced unfolding of isolated Gankryin involves a diverse set of pathways with a preference for a C- to N-terminus unfolding mechanism whereas this diversity is reduced upon complex formation with the central repeats, which are those most tightly bound to the ligand, tending to unfold last. Our study shows how stepwise unfolding can buffer repeat proteins and their binding partners from mechanical stress in the cell. It also points to a mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.
Collapse
Affiliation(s)
- Giovanni Settanni
- Physics Department, Johannes Gutenberg University, Mainz, Germany
- * E-mail: (GS); (EP); (LSI)
| | - David Serquera
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, United States of America
| | - Emanuele Paci
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail: (GS); (EP); (LSI)
| | - Laura S. Itzhaki
- University of Cambridge Department of Chemistry, Cambridge, United Kingdom
- * E-mail: (GS); (EP); (LSI)
| |
Collapse
|
27
|
Das D, Samanta D, Hasan S, Das A, Bhattacharya A, Dasgupta S, Chakrabarti A, Ghorai P, Das Gupta C. Identical RNA-protein interactions in vivo and in vitro and a scheme of folding the newly synthesized proteins by ribosomes. J Biol Chem 2012; 287:37508-21. [PMID: 22932895 DOI: 10.1074/jbc.m112.396127] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A distinct three-dimensional shape of rRNA inside the ribosome is required for the peptidyl transfer activity of its peptidyltransferase center (PTC). In contrast, even the in vitro transcribed PTC RNA interacts with unfolded protein(s) at about five sites to let them attain their native states. We found that the same set of conserved nucleotides in the PTC interact identically with nascent and chemically unfolded proteins in vivo and in vitro, respectively. The time course of this interaction, difficult to follow in vivo, was observed in vitro. It suggested nucleation of folding of cytosolic globular proteins vectorially from hydrophilic N to hydrophobic C termini, consistent with our discovery of a regular arrangement of cumulative hydrophobic indices of the peptide segments of cytosolic proteins from N to C termini. Based on this observation, we propose a model here for the nucleation of folding of the nascent protein chain by the PTC.
Collapse
Affiliation(s)
- Debasis Das
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, 92-A.P.C. Road, Kolkata 700 009, India
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Wang Y, Chu X, Suo Z, Wang E, Wang J. Multidomain protein solves the folding problem by multifunnel combined landscape: theoretical investigation of a Y-family DNA polymerase. J Am Chem Soc 2012; 134:13755-64. [PMID: 22827444 DOI: 10.1021/ja3045663] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Approximately three-fourths of eukaryotic proteins are composed of multiple independently folded domains. However, much of our understanding is based on single domain proteins or isolated domains whose studies directly lead to well-known energy landscape theory in which proteins fold by navigating through a funneled energy landscape toward native structure ensembles. The degrees of freedom for proteins with multiple domains are many orders of magnitude larger than that for single domain proteins. Now, the question arises: How do the multidomain proteins solve the "protein folding problem"? Here, we specifically address this issue by exploring the structure folding relationship of Sulfolobus solfataricus DNA polymerase IV (DPO4), a prototype Y-family DNA polymerase which contains a polymerase core consisting of a palm (P domain), a finger (F domain), and a thumb domain (T domain) in addition to a little finger domain (LF domain). The theoretical results are in good agreement with the experimental data and lead to several theoretical predictions. Finally, we propose that for rapid folding into well-defined conformations which carry out the biological functions, four-domain DPO4 employs a divide-and-conquer strategy, that is, combining multiple individual folding funnels into a single funnel (domains fold independently and then coalesce). In this way, the degrees of freedom for multidomain proteins are polynomial rather than exponential, and the conformational search process can be reduced effectively from a large to a smaller time scale.
Collapse
Affiliation(s)
- Yong Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China
| | | | | | | | | |
Collapse
|
29
|
Lee W, Strümpfer J, Bennett V, Schulten K, Marszalek PE. Mutation of conserved histidines alters tertiary structure and nanomechanics of consensus ankyrin repeats. J Biol Chem 2012; 287:19115-21. [PMID: 22514283 PMCID: PMC3365944 DOI: 10.1074/jbc.m112.365569] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The conserved TPLH tetrapeptide motif of ankyrin repeats (ARs) plays an important role in stabilizing AR proteins, and histidine (TPLH)-to-arginine (TPLR) mutations in this motif have been associated with a hereditary human anemia, spherocytosis. Here, we used a combination of atomic force microscopy-based single-molecule force spectroscopy and molecular dynamics simulations to examine the mechanical effects of His → Arg substitutions in TPLH motifs in a model AR protein, NI6C. Our molecular dynamics results show that the mutant protein is less mechanically stable than the WT protein. Our atomic force microscopy results indicate that the mechanical energy input necessary to fully unfold the mutant protein is only half of that necessary to unfold the WT protein (53 versus 106 kcal/mol). In addition, the ability of the mutant to generate refolding forces is also reduced. Moreover, the mutant protein subjected to cyclic stretch-relax measurements displays mechanical fatigue, which is absent in the WT protein. Taken together, these results indicate that the His → Arg substitutions in TPLH motifs compromise mechanical properties of ARs and suggest that the origin of hereditary spherocytosis may be related to mechanical failure of ARs.
Collapse
Affiliation(s)
- Whasil Lee
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | | | | | | | | |
Collapse
|
30
|
Lee W, Zeng X, Rotolo K, Yang M, Schofield CJ, Bennett V, Yang W, Marszalek PE. Mechanical anisotropy of ankyrin repeats. Biophys J 2012; 102:1118-26. [PMID: 22404934 DOI: 10.1016/j.bpj.2012.01.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 01/09/2012] [Accepted: 01/20/2012] [Indexed: 12/19/2022] Open
Abstract
Red blood cells are frequently deformed and their cytoskeletal proteins such as spectrin and ankyrin-R are repeatedly subjected to mechanical forces. While the mechanics of spectrin was thoroughly investigated in vitro and in vivo, little is known about the mechanical behavior of ankyrin-R. In this study, we combine coarse-grained steered molecular dynamics simulations and atomic force spectroscopy to examine the mechanical response of ankyrin repeats (ARs) in a model synthetic AR protein NI6C, and in the D34 fragment of native ankyrin-R when these proteins are subjected to various stretching geometry conditions. Our steered molecular dynamics results, supported by AFM measurements, reveal an unusual mechanical anisotropy of ARs: their mechanical stability is greater when their unfolding is forced to propagate from the N-terminus toward the C-terminus (repeats unfold at ~60 pN), as compared to the unfolding in the opposite direction (unfolding force ∼ 30 pN). This anisotropy is also reflected in the complex refolding behavior of ARs. The origin of this unfolding and refolding anisotropy is in the various numbers of native contacts that are broken and formed at the interfaces between neighboring repeats depending on the unfolding/refolding propagation directions. Finally, we discuss how these complex mechanical properties of ARs in D34 may affect its behavior in vivo.
Collapse
Affiliation(s)
- Whasil Lee
- Center for Biologically Inspired Materials and Material Systems and Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, USA
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Marszalek PE, Dufrêne YF. Stretching single polysaccharides and proteins using atomic force microscopy. Chem Soc Rev 2012; 41:3523-34. [DOI: 10.1039/c2cs15329g] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
32
|
Zhou R, He Y, Xiao Y. Multi-nucleation and vectorial folding pathways of large helix protein. Comput Biol Chem 2011; 35:169-73. [DOI: 10.1016/j.compbiolchem.2011.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/31/2011] [Accepted: 04/17/2011] [Indexed: 11/30/2022]
|