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Moreau A, Yaya F, Lu H, Surendranath A, Charrier A, Dehapiot B, Helfer E, Viallat A, Peng Z. Physical mechanisms of red blood cell splenic filtration. Proc Natl Acad Sci U S A 2023; 120:e2300095120. [PMID: 37874856 PMCID: PMC10622898 DOI: 10.1073/pnas.2300095120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/02/2023] [Indexed: 10/26/2023] Open
Abstract
The splenic interendothelial slits fulfill the essential function of continuously filtering red blood cells (RBCs) from the bloodstream to eliminate abnormal and aged cells. To date, the process by which 8 [Formula: see text]m RBCs pass through 0.3 [Formula: see text]m-wide slits remains enigmatic. Does the slit caliber increase during RBC passage as sometimes suggested? Here, we elucidated the mechanisms that govern the RBC retention or passage dynamics in slits by combining multiscale modeling, live imaging, and microfluidic experiments on an original device with submicron-wide physiologically calibrated slits. We observed that healthy RBCs pass through 0.28 [Formula: see text]m-wide rigid slits at 37 °C. To achieve this feat, they must meet two requirements. Geometrically, their surface area-to-volume ratio must be compatible with a shape in two tether-connected equal spheres. Mechanically, the cells with a low surface area-to-volume ratio (28% of RBCs in a 0.4 [Formula: see text]m-wide slit) must locally unfold their spectrin cytoskeleton inside the slit. In contrast, activation of the mechanosensitive PIEZO1 channel is not required. The RBC transit time through the slits follows a [Formula: see text]1 and [Formula: see text]3 power law with in-slit pressure drop and slip width, respectively. This law is similar to that of a Newtonian fluid in a two-dimensional Poiseuille flow, showing that the dynamics of RBCs is controlled by their cytoplasmic viscosity. Altogether, our results show that filtration through submicron-wide slits is possible without further slit opening. Furthermore, our approach addresses the critical need for in vitro evaluation of splenic clearance of diseased or engineered RBCs for transfusion and drug delivery.
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Affiliation(s)
- Alexis Moreau
- Aix Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Turing Centre for Living Systems, Marseille13009, France
| | - François Yaya
- Aix Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Turing Centre for Living Systems, Marseille13009, France
| | - Huijie Lu
- Richard and Loan Hill Department of Biomedical Engineering, University of Illinois, Chicago, IL60612
| | - Anagha Surendranath
- Aix Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Turing Centre for Living Systems, Marseille13009, France
| | - Anne Charrier
- Aix Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Turing Centre for Living Systems, Marseille13009, France
| | - Benoit Dehapiot
- Aix Marseille Université, CNRS, Institut de Biologie du Développement de Marseille, Turing Centre for Living Systems, Marseille13009, France
| | - Emmanuèle Helfer
- Aix Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Turing Centre for Living Systems, Marseille13009, France
| | - Annie Viallat
- Aix Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Turing Centre for Living Systems, Marseille13009, France
| | - Zhangli Peng
- Richard and Loan Hill Department of Biomedical Engineering, University of Illinois, Chicago, IL60612
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2
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Rivera M, Mjaavatten A, Smith SB, Baez M, Wilson CAM. Temperature dependent mechanical unfolding and refolding of a protein studied by thermo-regulated optical tweezers. Biophys J 2023; 122:513-521. [PMID: 36587240 PMCID: PMC9941719 DOI: 10.1016/j.bpj.2022.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
Temperature is a useful system variable to gather kinetic and thermodynamic information from proteins. Usually, free energy and the associated entropic and enthalpic contributions are obtained by quantifying the conformational equilibrium based on melting experiments performed in bulk conditions. Such experiments are suitable only for those small single-domain proteins whose side reactions of irreversible aggregation are unlikely to occur. Here, we avoid aggregation by pulling single-protein molecules in a thermo-regulated optical tweezers. Thus, we are able to explore the temperature dependence of the thermodynamic and kinetic parameters of MJ0366 from Methanocaldococcus jannaschii at the single-molecule level. By performing force-ramp experiments between 2°C and 40°C, we found that MJ0366 has a nonlinear dependence of free energy with temperature and a specific heat change of 2.3 ± 1.2 kcal/mol∗K. These thermodynamic parameters are compatible with a two-state unfolding/refolding mechanism for MJ0366. However, the kinetics measured as a function of the temperature show a complex behavior, suggesting a three-state folding mechanism comprising a high-energy intermediate state. The combination of two perturbations, temperature and force, reveals a high-energy species in the folding mechanism of MJ0366 not detected in force-ramp experiments at constant temperature.
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Affiliation(s)
- Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | | | | | - Mauricio Baez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
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3
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The spectrin cytoskeleton integrates endothelial mechanoresponses. Nat Cell Biol 2022; 24:1226-1238. [PMID: 35817960 DOI: 10.1038/s41556-022-00953-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/01/2022] [Indexed: 12/13/2022]
Abstract
Physiological blood flow induces the secretion of vasoactive compounds, notably nitric oxide, and promotes endothelial cell elongation and reorientation parallel to the direction of applied shear. How shear is sensed and relayed to intracellular effectors is incompletely understood. Here, we demonstrate that an apical spectrin network is essential to convey the force imposed by shear to endothelial mechanosensors. By anchoring CD44, spectrins modulate the cell surface density of hyaluronan and sense and translate shear into changes in plasma membrane tension. Spectrins also regulate the stability of apical caveolae, where the mechanosensitive PIEZO1 channels are thought to reside. Accordingly, shear-induced PIEZO1 activation and the associated calcium influx were absent in spectrin-deficient cells. As a result, cell realignment and flow-induced endothelial nitric oxide synthase stimulation were similarly dependent on spectrin. We conclude that the apical spectrin network is not only required for shear sensing but also transmits and distributes the resulting tensile forces to mechanosensors that elicit protective and vasoactive responses.
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4
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Gil-Redondo JC, Weber A, Toca-Herrera JL. Measuring (biological) materials mechanics with atomic force microscopy. 3. Mechanical unfolding of biopolymers. Microsc Res Tech 2022; 85:3025-3036. [PMID: 35502131 PMCID: PMC9543778 DOI: 10.1002/jemt.24136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Biopolymers, such as polynucleotides, polypeptides and polysaccharides, are macromolecules that direct most of the functions in living beings. Studying the mechanical unfolding of biopolymers provides important information about their molecular elasticity and mechanical stability, as well as their energy landscape, which is especially important in proteins, since their three‐dimensional structure is essential for their correct activity. In this primer, we present how to study the mechanical properties of proteins with atomic force microscopy and how to obtain information about their stability and energetic landscape. In particular, we discuss the preparation of polyprotein constructs suitable for AFM single molecule force spectroscopy (SMFS), describe the parameters used in our force‐extension SMFS experiments and the models and equations employed in the analysis of the data. As a practical example, we show the effect of the temperature on the unfolding force, the distance to the transition state, the unfolding rate at zero force, the height of the transition state barrier, and the spring constant of the protein for a construct containing nine repeats of the I27 domain from the muscle protein titin.
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Affiliation(s)
- Juan Carlos Gil-Redondo
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - Andreas Weber
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
| | - José L Toca-Herrera
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
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5
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Singh S, Ponnappan N, Verma A, Mittal A. Osmotic tolerance of avian erythrocytes to complete hemolysis in solute free water. Sci Rep 2019; 9:7976. [PMID: 31138851 PMCID: PMC6538707 DOI: 10.1038/s41598-019-44487-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/17/2019] [Indexed: 01/17/2023] Open
Abstract
Osmotic behavior of erythrocytes is not only important clinically, but is also significant in understanding of material transport across biological membranes. It is most commonly studied through fragiligrams – plots of the degree of hemolysis as a function of extracellular osmolarity. A fundamental assumption in experimental and theoretical studies on osmolarity driven transport of water across the plasma membranes of all cells is the sigmoidal nature of their osmotic behavior. Sigmoidal data is mathematically monotonic showing either a decreasing only or an increasing only trend, but not both, within certain thresholds; beyond these thresholds the data is asymptotic or flat. Fragiligrams of erythrocytes are usually sigmoidal, with maximal hemolysis in plain solute-free water and often up to a certain extracellular hypotonic environment. In this work, we report a new discovery of non-monotonic osmotic behavior of avian erythrocytes. In contrast to the expected monotonic fragiligrams obtained for mammalian erythrocytes, fragiligrams of avian erythrocytes show non-monotonic curves. Maximal hemolysis of avian erythrocytes was not observed at the most hypotonic conditions – instead, maximal hemolysis was observed at mild hypotonic conditions. Hemolysis of avian erythrocytes first increases then decreases with increasing extracellular osmolarity. We also report that the non-monotonic fragiligrams of chicken erythrocytes are converted to the expected monotonic sigmoids subsequent to controlled extracellular trypsinization. While possibly having profound evolutionary implications for vertebrates, the findings reported in this work have a direct impact on understanding of avian physiology. Our results also compel revisiting of experimental and theoretical models for understanding material transport across biological membranes under different osmotic conditions.
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Affiliation(s)
- Snigdha Singh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India
| | - Nisha Ponnappan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India
| | - Anand Verma
- National Institute of Pathology - Indian Council of Medical Research (ICMR), New Delhi, 110029, India.,Green trace consulting Pvt Ltd, Delhi, 110096, India
| | - Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India.
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6
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Distinct mechanical properties in homologous spectrin-like repeats of utrophin. Sci Rep 2019; 9:5210. [PMID: 30914715 PMCID: PMC6435810 DOI: 10.1038/s41598-019-41569-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 03/12/2019] [Indexed: 11/09/2022] Open
Abstract
Patients with Duchenne muscular dystrophy (DMD) lack the protein dystrophin, which is a critical molecular component of the dystrophin-glycoprotein complex (DGC). Dystrophin is hypothesized to function as a molecular shock absorber that mechanically stabilizes the sarcolemma of striated muscle through interaction with the cortical actin cytoskeleton via its N-terminal half and with the transmembrane protein β-dystroglycan via its C-terminal region. Utrophin is a fetal homologue of dystrophin that can subserve many dystrophin functions and is therefore under active investigation as a dystrophin replacement therapy for DMD. Here, we report the first mechanical characterization of utrophin using atomic force microscopy (AFM). Our data indicate that the mechanical properties of spectrin-like repeats in utrophin are more in line with the PEVK and Ig-like repeats of titin rather than those reported for repeats in spectrin or dystrophin. Moreover, we measured markedly different unfolding characteristics for spectrin repeats within the N-terminal actin-binding half of utrophin compared to those in the C-terminal dystroglycan-binding half, even though they exhibit identical thermal denaturation profiles. Our results demonstrate dramatic differences in the mechanical properties of structurally homologous utrophin constructs and suggest that utrophin may function as a stiff elastic element in series with titin at the myotendinous junction.
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7
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Bhattacharya S, Ainavarapu SRK. Mechanical Softening of a Small Ubiquitin-Related Modifier Protein Due to Temperature Induced Flexibility at the Core. J Phys Chem B 2018; 122:9128-9136. [PMID: 30204456 DOI: 10.1021/acs.jpcb.8b06844] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite the growing interest in the thermal softening of proteins, the mechanistic details of it are far from understood. β-Grasp proteins have globular shape with compact structure and they are mechanically resilient. The β-clamp or mechanical clamp in them formed by the interactions between the terminal β-strands is generally associated with the protein mechanical resistance. Although previous studies showed that temperature can perturb the protein mechanical stability, the structural changes leading to the lowered mechanical resistance are not known. Here, we investigated the temperature dependent mechanical stability of small ubiquitin-related modifier 2 (SUMO2) using single-molecule force spectroscopy (SMFS) and the corresponding conformational changes using ensemble experiments. SMFS studies on the polyprotein of SUMO2 estimate a decrease in the spring constant of the protein from 4.50 to 1.35 N/m upon increasing the temperature from 5 to 45 °C. Interestingly, near-UV circular dichroism spectroscopy reveals a decrease in tertiary structure content while the overall secondary structure of the protein remains unchanged. Steady-state fluorescence and quenching studies on SUMO2 with a tryptophan mutation at the core (F60W) show that the nonpolar environment of the tryptophan is unchanged and the protein core is inaccessible to the bulk solvent, in the same temperature range. We attribute the thermal softening observed in atomic force microscopy (AFM) experiments to the reduction in tertiary structure of SUMO2. Our results provide evidence for the importance of the intramolecular interactions at the protein core along with the β-clamp or mechanical clamp in providing the mechanical resistance as well as in modulating the protein stiffness.
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Affiliation(s)
- Shrabasti Bhattacharya
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Dr Homi Bhabha Road , Colaba, Mumbai 400005 , India
| | - Sri Rama Koti Ainavarapu
- Department of Chemical Sciences , Tata Institute of Fundamental Research , Dr Homi Bhabha Road , Colaba, Mumbai 400005 , India
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8
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Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17. J Struct Biol 2017; 201:162-170. [PMID: 29221897 DOI: 10.1016/j.jsb.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/08/2017] [Accepted: 12/04/2017] [Indexed: 11/20/2022]
Abstract
Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicellular organisms and are of potential value in nanotechnology. To reveal the unique physical features of repeat proteins we have studied the structural and mechanical properties of three repeats of chicken brain α-spectrin (R15, R16 and R17) at the atomic level under stretching at constant velocities (0.01, 0.05 and 0.1 Å·ps-1) and constant forces (700 and 900 pN) using molecular dynamics (MD) simulations at T = 300 K. 114 independent MD simulations were performed and their analysis has been done. Despite structural similarity of these domains we have found that R15 is less mechanically stable than R16, which is less stable than R17. This result is in agreement with the thermal unfolding rates. Moreover, we have observed the relationship between mechanical stability, flexibility of the domains and the number of aromatic residues involved in aromatic clusters.
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9
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Basu A, Harper S, Pesciotta EN, Speicher KD, Chakrabarti A, Speicher DW. Proteome analysis of the triton-insoluble erythrocyte membrane skeleton. J Proteomics 2015; 128:298-305. [PMID: 26271157 DOI: 10.1016/j.jprot.2015.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/24/2015] [Accepted: 08/05/2015] [Indexed: 12/13/2022]
Abstract
Erythrocyte shape and membrane integrity is imparted by the membrane skeleton, which can be isolated as a Triton X-100 insoluble structure that retains the biconcave shape of intact erythrocytes, indicating isolation of essentially intact membrane skeletons. These erythrocyte "Triton Skeletons" have been studied morphologically and biochemically, but unbiased proteome analysis of this substructure of the membrane has not been reported. In this study, different extraction buffers and in-depth proteome analyses were used to more fully define the protein composition of this functionally critical macromolecular complex. As expected, the major, well-characterized membrane skeleton proteins and their associated membrane anchors were recovered in good yield. But surprisingly, a substantial number of additional proteins that are not considered in erythrocyte membrane skeleton models were recovered in high yields, including myosin-9, lipid raft proteins (stomatin, flotillin1 and 2), multiple chaperone proteins (HSPs, protein disulfide isomerase and calnexin), and several other proteins. These results show that the membrane skeleton is substantially more complex than previous biochemical studies indicated, and it apparently has localized regions with unique protein compositions and functions. This comprehensive catalog of the membrane skeleton should lead to new insights into erythrocyte membrane biology and pathogenic mutations that perturb membrane stability. Biological significance Current models of erythrocyte membranes describe fairly simple homogenous structures that are incomplete. Proteome analysis of the erythrocyte membrane skeleton shows that it is quite complex and includes a substantial number of proteins whose roles and locations in the membrane are not well defined. Further elucidation of interactions involving these proteins and definition of microdomains in the membrane that contain these proteins should yield novel insights into how the membrane skeleton produces the normal biconcave erythrocyte shape and how it is perturbed in pathological conditions that destabilize the membrane.
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Affiliation(s)
- Avik Basu
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA; Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Sandra Harper
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Esther N Pesciotta
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kaye D Speicher
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - David W Speicher
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA.
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10
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Xiao S, Gräter F. Molecular basis of the mechanical hierarchy in myomesin dimers for sarcomere integrity. Biophys J 2015; 107:965-73. [PMID: 25140432 PMCID: PMC4142248 DOI: 10.1016/j.bpj.2014.06.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/26/2014] [Accepted: 06/16/2014] [Indexed: 01/08/2023] Open
Abstract
Myomesin is one of the most important structural molecules constructing the M-band in the force-generating unit of striated muscle, and a critical structural maintainer of the sarcomere. Using molecular dynamics simulations, we here dissect the mechanical properties of the structurally known building blocks of myomesin, namely α-helices, immunoglobulin (Ig) domains, and the dimer interface at myomesin's 13th Ig domain, covering the mechanically important C-terminal part of the molecule. We find the interdomain α-helices to be stabilized by the hydrophobic interface formed between the N-terminal half of these helices and adjacent Ig domains, and, interestingly, to show a rapid unfolding and refolding equilibrium especially under low axial forces up to ∼ 15 pN. These results support and yield atomic details for the notion of recent atomic-force microscopy experiments, namely, that the unique helices inserted between Ig domains in myomesin function as elastomers and force buffers. Our results also explain how the C-terminal dimer of two myomesin molecules is mechanically outperforming the helices and Ig domains in myomesin and elsewhere, explaining former experimental findings. This study provides a fresh view onto how myomesin integrates elastic helices, rigid immunoglobulin domains, and an extraordinarily resistant dimer into a molecular structure, to feature a mechanical hierarchy that represents a firm and yet extensible molecular anchor to guard the stability of the sarcomere.
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Affiliation(s)
- Senbo Xiao
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Chinese Academy of Sciences-Max-Planck-Society Partner Institute and Key Laboratory for Computational Biology, Shanghai, China; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany.
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11
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Cost AL, Ringer P, Chrostek-Grashoff A, Grashoff C. How to Measure Molecular Forces in Cells: A Guide to Evaluating Genetically-Encoded FRET-Based Tension Sensors. Cell Mol Bioeng 2014; 8:96-105. [PMID: 25798203 PMCID: PMC4361753 DOI: 10.1007/s12195-014-0368-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/21/2014] [Indexed: 12/16/2022] Open
Abstract
The ability of cells to sense and respond to mechanical forces is central to a wide range of biological processes and plays an important role in numerous pathologies. The molecular mechanisms underlying cellular mechanotransduction, however, have remained largely elusive because suitable methods to investigate subcellular force propagation were missing. Here, we review recent advances in the development of biosensors that allow molecular force measurements. We describe the underlying principle of currently available techniques and propose a strategy to systematically evaluate new Förster resonance energy transfer (FRET)-based biosensors.
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Affiliation(s)
- Anna-Lena Cost
- Group of Molecular Mechanotransduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152 Germany
| | - Pia Ringer
- Group of Molecular Mechanotransduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152 Germany
| | - Anna Chrostek-Grashoff
- Group of Molecular Mechanotransduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152 Germany
| | - Carsten Grashoff
- Group of Molecular Mechanotransduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152 Germany
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12
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13
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Koirala D, Punnoose JA, Shrestha P, Mao H. Yoctoliter thermometry for single-molecule investigations: a generic bead-on-a-tip temperature-control module. Angew Chem Int Ed Engl 2014; 53:3470-4. [PMID: 24596309 DOI: 10.1002/anie.201310172] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/06/2014] [Indexed: 11/10/2022]
Abstract
A new temperature-jump (T-jump) strategy avoids photo-damage of individual molecules by focusing a low-intensity laser on a black microparticle at the tip of a capillary. The black particle produces an efficient photothermal effect that enables a wide selection of lasers with powers in the milliwatt range to achieve a T-jump of 65 °C within milliseconds. To measure the temperature in situ in single-molecule experiments, the temperature-dependent mechanical unfolding of a single DNA hairpin molecule was monitored by optical tweezers within a yoctoliter volume. Using this bead-on-a-tip module and the robust single-molecule thermometer, full thermodynamic landscapes for the unfolding of this DNA hairpin were retrieved. These approaches are likely to provide powerful tools for the microanalytical investigation of dynamic processes with a combination of T-jump and single-molecule techniques.
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Affiliation(s)
- Deepak Koirala
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242 (USA)
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14
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Koirala D, Punnoose JA, Shrestha P, Mao H. Yoctoliter Thermometry for Single-Molecule Investigations: A Generic Bead-on-a-Tip Temperature-Control Module. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Glyakina AV, Balabaev NK, Galzitskaya OV. Experimental and theoretical studies of mechanical unfolding of different proteins. BIOCHEMISTRY (MOSCOW) 2014; 78:1216-27. [PMID: 24460936 DOI: 10.1134/s0006297913110023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mechanical properties of proteins are important for a wide range of biological processes including cell adhesion, muscle contraction, and protein translocation across biological membranes. It is necessary to reveal how proteins achieve their required mechanical stability under natural conditions in order to understand the biological processes and also to use the knowledge for constructing new biomaterials for medical and industrial purposes. In this connection, it is important to know how a protein will behave in response to various impacts. Theoretical and experimental works on mechanical unfolding of globular proteins will be considered in detail in this review.
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Affiliation(s)
- A V Glyakina
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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16
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Thermo-mechanical properties of the cell surface assessed by atomic force microscopy. Micron 2012; 43:1232-8. [DOI: 10.1016/j.micron.2012.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 03/30/2012] [Accepted: 04/01/2012] [Indexed: 01/22/2023]
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17
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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.
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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
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18
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Afrin R, Nakaji M, Sekiguchi H, Lee D, Kishimoto K, Ikai A. Forced extension of delipidated red blood cell cytoskeleton with little indication of spectrin unfolding. Cytoskeleton (Hoboken) 2012; 69:101-12. [DOI: 10.1002/cm.21001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/06/2011] [Accepted: 12/20/2011] [Indexed: 11/07/2022]
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19
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Computational investigation of the effect of thermal perturbation on the mechanical unfolding of titin I27. J Mol Model 2011; 18:2823-9. [PMID: 22119788 DOI: 10.1007/s00894-011-1298-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 11/02/2011] [Indexed: 10/15/2022]
Abstract
The emergence of single-molecule force measurement experiments has facilitated a better understanding of protein folding pathways and the thermodynamics involved. Computational methods such as steered molecular dynamics (SMD) simulations are helpful in providing atomistic level information on the unfolding pathways. Recent experimental studies have showed that combinations of single-molecule experiments with traditional methods such as chemical and/or thermal denaturation yield additional insights into the folding phenomenon. In this study, we report results from extensive computations (a total of about 60 SMD simulations with a total length of about 0.4 μs) that address the effect of thermal perturbation on the mechanical stability of the I27 domain of the protein titin. A wide range of temperatures (280-340 K) were considered for the pulling, which was done at both constant velocity and constant force using SMD simulations. Good agreement with experimental data, such as for the trends in changes in average force and the maximum force with respect to the temperature, was obtained. This study identifies two competing pathways for the mechanical unfolding of I27, and illustrates the significance of combining various techniques to examine protein folding.
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20
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Sanz-Herrera JA, Reina-Romo E. Cell-biomaterial mechanical interaction in the framework of tissue engineering: insights, computational modeling and perspectives. Int J Mol Sci 2011; 12:8217-44. [PMID: 22174660 PMCID: PMC3233466 DOI: 10.3390/ijms12118217] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 10/19/2011] [Accepted: 11/02/2011] [Indexed: 01/09/2023] Open
Abstract
Tissue engineering is an emerging field of research which combines the use of cell-seeded biomaterials both in vitro and/or in vivo with the aim of promoting new tissue formation or regeneration. In this context, how cells colonize and interact with the biomaterial is critical in order to get a functional tissue engineering product. Cell-biomaterial interaction is referred to here as the phenomenon involved in adherent cells attachment to the biomaterial surface, and their related cell functions such as growth, differentiation, migration or apoptosis. This process is inherently complex in nature involving many physico-chemical events which take place at different scales ranging from molecular to cell body (organelle) levels. Moreover, it has been demonstrated that the mechanical environment at the cell-biomaterial location may play an important role in the subsequent cell function, which remains to be elucidated. In this paper, the state-of-the-art research in the physics and mechanics of cell-biomaterial interaction is reviewed with an emphasis on focal adhesions. The paper is focused on the different models developed at different scales available to simulate certain features of cell-biomaterial interaction. A proper understanding of cell-biomaterial interaction, as well as the development of predictive models in this sense, may add some light in tissue engineering and regenerative medicine fields.
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Affiliation(s)
- Jose A. Sanz-Herrera
- School of Engineering, University of Seville, Camino de los descubrimientos s/n, 41092 Seville, Spain; E-Mail:
| | - Esther Reina-Romo
- School of Engineering, University of Seville, Camino de los descubrimientos s/n, 41092 Seville, Spain; E-Mail:
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21
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Simon DN, Wilson KL. The nucleoskeleton as a genome-associated dynamic 'network of networks'. Nat Rev Mol Cell Biol 2011; 12:695-708. [PMID: 21971041 DOI: 10.1038/nrm3207] [Citation(s) in RCA: 222] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the cytosol, actin polymers, intermediate filaments and microtubules can anchor to cell surface adhesions and interlink to form intricate networks. This cytoskeleton is anchored to the nucleus through LINC (links the nucleoskeleton and cytoskeleton) complexes that span the nuclear envelope and in turn anchor to networks of filaments in the nucleus. The metazoan nucleoskeleton includes nuclear pore-linked filaments, A-type and B-type lamin intermediate filaments, nuclear mitotic apparatus (NuMA) networks, spectrins, titin, 'unconventional' polymers of actin and at least ten different myosin and kinesin motors. These elements constitute a poorly understood 'network of networks' that dynamically reorganizes during mitosis and is responsible for genome organization and integrity.
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Affiliation(s)
- Dan N Simon
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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22
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Force spectroscopy 101: how to design, perform, and analyze an AFM-based single molecule force spectroscopy experiment. Curr Opin Chem Biol 2011; 15:710-8. [DOI: 10.1016/j.cbpa.2011.07.020] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/26/2011] [Accepted: 07/27/2011] [Indexed: 11/17/2022]
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23
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Popa I, Fernández JM, Garcia-Manyes S. Direct quantification of the attempt frequency determining the mechanical unfolding of ubiquitin protein. J Biol Chem 2011; 286:31072-9. [PMID: 21768096 PMCID: PMC3173078 DOI: 10.1074/jbc.m111.264093] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/05/2011] [Indexed: 11/06/2022] Open
Abstract
Understanding protein dynamics requires a comprehensive knowledge of the underlying potential energy surface that governs the motion of each individual protein molecule. Single molecule mechanical studies have provided the unprecedented opportunity to study the individual unfolding pathways along a well defined coordinate, the end-to-end length of the protein. In these experiments, unfolding requires surmounting an energy barrier that separates the native from the extended state. The calculation of the absolute value of the barrier height has traditionally relied on the assumption of an attempt frequency, υ(‡). Here we used single molecule force-clamp spectroscopy to directly determine the value of υ(‡) for mechanical unfolding by measuring the unfolding rate of the small protein ubiquitin at varying temperatures. Our experiments demonstrate a significant effect of the temperature on the mechanical rate of unfolding. By extrapolating the unfolding rate in the absence of force for different temperatures, varying within the range spanning from 5 to 45 °C, we measured a value for the activation barrier of ΔG(‡) = 71 ± 5 kJ/mol and an exponential prefactor υ(‡) ∼4 × 10(9) s(-1). Although the measured prefactor value is 3 orders of magnitude smaller than the value predicted by the transition state theory (∼6 × 10(12) s(-1)), it is 400-fold higher than that encountered in analogous experiments studying the effect of temperature on the reactivity of a protein-embedded disulfide bond (∼10(7) M(-1) s(-1)). This approach will allow quantitative characterization of the complete energy landscape of a folding polypeptide from highly extended states, of capital importance for proteins with elastic function.
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Affiliation(s)
- Ionel Popa
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Julio M. Fernández
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Sergi Garcia-Manyes
- From the Department of Biological Sciences, Columbia University, New York, New York 10027
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24
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The Nonlinear Structure of the Desmoplakin Plakin Domain and the Effects of Cardiomyopathy-Linked Mutations. J Mol Biol 2011; 411:1049-61. [DOI: 10.1016/j.jmb.2011.06.047] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/21/2011] [Accepted: 06/28/2011] [Indexed: 11/15/2022]
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25
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Haward SJ, Shewry PR, Marsh J, Miles MJ, Mc Master TJ. Force spectroscopy of an elastic peptide: effect of D₂O and temperature on persistence length. Microsc Res Tech 2011; 74:170-6. [PMID: 21275005 DOI: 10.1002/jemt.20888] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This study explores the mechanical unfolding of elastic protein analogues as a function of temperature, in both H₂O and D₂O, using atomic force microscopy (AFM) force spectroscopy in a specially constructed AFM liquid cell. This represents the first time that the effect of D₂O on protein flexibility has been investigated at the single molecule level by this technique. Model elastic peptides, R6, were encoded from synthetic genes expressed in Escherichia coli. The peptides possess short N- and C-terminal domains with central repetitive domains containing 13 repeats of the motif PGQGQQ-plus-GYYPTSLQQ. These sequences mimic those in native high molecular weight subunit glutenin proteins which confer elasticity to bread dough. Fitting single molecule stretching events to the worm-like chain model, allows determination of the molecular persistence length under various experimental conditions. The effect of increasing the temperature is to increase the persistence length of the peptide in both H₂O and D₂O, consistent with the expected "thermal softening" effect. However, the effect is significantly enhanced in D₂O, in which the persistence length at 45°C is ∼25% greater than the value measured in H₂O at the same temperature. Stronger intrapeptide H-bonding due to isotopic substitution of hydrogen for deuterium is the most likely cause of the enhanced backbone rigidity.
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Affiliation(s)
- Simon J Haward
- H. H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom.
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26
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Meng F, Sachs F. Visualizing dynamic cytoplasmic forces with a compliance-matched FRET sensor. J Cell Sci 2010; 124:261-9. [PMID: 21172803 DOI: 10.1242/jcs.071928] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Mechanical forces are ubiquitous modulators of cell activity but little is known about the mechanical stresses in the cell. Genetically encoded FRET-based force sensors now allow the measurement of local stress in specific host proteins in vivo in real time. For a minimally invasive probe, we designed one with a mechanical compliance matching that of many common cytoskeleton proteins. sstFRET is a cassette composed of Venus and Cerulean linked by a spectrin repeat. The stress sensitivity of the probe was measured in solution using DNA springs to push the donor and acceptor apart with 5-7 pN and this produced large changes in FRET. To measure cytoskeletal stress in vivo we inserted sstFRET into α-actinin and expressed it in HEK and BAEC cells. Time-lapse imaging showed the presence of stress gradients in time and space, often uncorrelated with obvious changes in cell shape. The gradients could be rapidly relaxed by thrombin-induced cell contraction associated with inhibition of myosin II. The tension in actinin fluctuated rapidly (scale of seconds) illustrating a cytoskeleton in dynamic equilibrium. Stress in the cytoskeleton can be driven by macroscopic stresses applied to the cell. Using sstFRET as a tool to measure internal stress, we tested the prediction that osmotic pressure increases cytoskeletal stress. As predicted, hypotonic swelling increased the tension in actinin, confirming the model derived from AFM. Anisotonic stress also produced a novel transient (~2 minutes) decrease in stress upon exposure to a hypotonic challenge, matched by a transient increase with hypertonic stress. This suggests that, at rest, the stress axis of actinin is not parallel to the stress axis of actin and that swelling can reorient actinin to lie more parallel where it can absorb a larger fraction of the total stress. Protein stress sensors are opening new perspectives in cell biology.
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Affiliation(s)
- Fanjie Meng
- Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA
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27
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Siódmiak J, Santamaría-Holek I, Gadomski A. On morphological selection rule of noisy character applied to model (dis)orderly protein formations. J Chem Phys 2010; 132:195103. [DOI: 10.1063/1.3431196] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Nanomechanics of multiple units in the erythrocyte membrane skeletal network. Ann Biomed Eng 2010; 38:2956-67. [PMID: 20490687 PMCID: PMC2914261 DOI: 10.1007/s10439-010-0040-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 04/06/2010] [Indexed: 11/23/2022]
Abstract
Erythrocytes undergo deformations when they transport O2 and CO2 across the membrane, yet the 3D nanomechanics of the skeletal network remains poorly understood. Expanding from our previous single isolated unit, we now simulate networks consisting of 1–10 concentric rings of repeating units in equibiaxial deformation. The networks are organized with (1) a 3D model for a single unit, (2) a wrap-around mode between Sp and actin protofilament in the intra-unit interaction, and (3) a random inter-unit connectivity. These assumptions permit efficient five-degrees-of-freedom (5DOF) simulations when up to 30 pN of radial forces are applied to the boundary spectrin (Sp) and the center and other units are analyzed. As 6 Sp balance their tensions, hexagonal units become irregular. While actin protofilaments remain tangent to the network, their yaw (Φ) angles change drastically with addition of neighboring units or an Sp unfolding. It is anticipated that during deformation, transmembrane complexes associated with the network move laterally through the lipid bilayer and increase the diffusion of molecules across the membrane. When protofilament/Sp sweeps under the lipid bilayer, they mix up the submembrane concentration gradient. Thus, the nanomechanics of actin protofilaments and Sp may enhance the transport of molecules during erythrocyte deformation.
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29
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Zhong Z, Chang SA, Kalinowski A, Wilson KL, Dahl KN. Stabilization of the spectrin-like domains of nesprin-1α by the evolutionarily conserved "adaptive" domain. Cell Mol Bioeng 2010; 3:139-150. [PMID: 20563238 DOI: 10.1007/s12195-010-0121-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Nesprins are located at the outer and inner membranes of the nuclear envelope and help link the cytoskeleton to the nucleoskeleton. Nesprin-1α, located at the inner nuclear membrane, binds to A-type lamins and emerin and has homology to spectrin-repeat proteins. However, the mechanical and thermodynamic properties of the spectrin-like repeats (SLRs) of nesprin-1α and the potential structural contributions of the unique central domain were untested. In other spectrin superfamily proteins, tandem spectrin-repeat domains undergo cooperatively coupled folding and unfolding. We hypothesized that the large central domain, which interrupts SLRs and is conserved in other nesprin isoforms, might confer unique structural properties. To test this model we measured the thermal unfolding of nesprin-1α fragments using circular dichroism and dynamic light scattering. The SLRs in nesprin-1α were found to have structural and thermodynamic properties typical of spectrins. The central domain had relatively little secondary structure as an isolated fragment, but significantly stabilized larger SLR-containing molecules by increasing their overall helicity, thermal stability and cooperativity of folding. We suggest this domain, now termed the 'adaptive' domain (AD), also strengthens dimerization and inhibits unfolding. Further engineering of the isolated AD, and AD-containing nesprin molecules, may yield new information about the higher-order association of cooperative protein motifs.
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Affiliation(s)
- Zhixia Zhong
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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30
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Dupres V, Alsteens D, Wilk S, Hansen B, Heinisch JJ, Dufrêne YF. The yeast Wsc1 cell surface sensor behaves like a nanospring in vivo. Nat Chem Biol 2009; 5:857-62. [DOI: 10.1038/nchembio.220] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 07/13/2009] [Indexed: 01/06/2023]
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31
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Abstract
Physical factors drive evolution and play important roles in motility and attachment as well as in differentiation. As animal cells adhere to survive, they generate force and 'feel' various mechanical features of their surroundings, with mechanosensory mechanisms based in part on force-induced conformational changes. Single-molecule methods for in vitro nano-manipulation, together with new in situ proteomic approaches that exploit mass spectrometry, are helping to identify and characterize the molecules and mechanics of structural transitions within cells and matrices. Given the diversity of cell and molecular responses, networks of biomolecules with conformations and interactions sculpted by force seem more likely than singular mechanosensors. Elaboration of the proteins that unfold and change structure in the extracellular matrix and in cells is needed - particularly with regard to the force-driven kinetics - in order to understand the systems biology of signaling in development, differentiation, and disease.
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Affiliation(s)
- André E X Brown
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
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32
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Ackbarow T, Keten S, Buehler MJ. A multi-timescale strength model of alpha-helical protein domains. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:035111. [PMID: 21817269 DOI: 10.1088/0953-8984/21/3/035111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Here we report a constitutive model that characterizes the strength of an alpha-helical protein domain subjected to tensile deformation, covering more than ten orders of magnitude in timescales. The model elucidates multiple physical mechanisms of failure in dependence on the deformation rate, quantitatively linking atomistic simulation results with experimental strength measurements of alpha-helical protein domains. The model provides a description of the strength of alpha-helices based on fundamental physical parameters such as the H-bond energy and the polypeptide's persistence length, showing that strength is controlled by energetic, nonequilibrium processes at high rates and by thermodynamical, equilibrium processes at low rates. Our model provides a novel perspective on the strength of protein domains at ultra-slow pulling speeds relevant under physiologic and experimental conditions.
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Affiliation(s)
- Theodor Ackbarow
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue Room 1-235A&B, Cambridge, MA, USA. Max-Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
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33
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Czogalla A, Grzymajło K, Jezierski A, Sikorski AF. Phospholipid-induced structural changes to an erythroid β spectrin ankyrin-dependent lipid-binding site. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2612-20. [DOI: 10.1016/j.bbamem.2008.07.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Revised: 07/01/2008] [Accepted: 07/18/2008] [Indexed: 12/01/2022]
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34
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The effect of temperature on mechanical resistance of the native and intermediate states of I27. Biophys J 2008; 95:5296-305. [PMID: 18775959 DOI: 10.1529/biophysj.108.141275] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated the effect of temperature on the mechanical unfolding of I27 from human cardiac titin, employing a custom-built temperature control device for single-molecule atomic force microscopy measurement. A sawtooth pattern was observed in the force curves where each force peak reports on the unfolding of an I27 domain. In early unfolding events, we observed a "hump-like" deviation due to the detachment of beta-strand A from each I27 domain. The force at which the humps appear was approximately 130 pN and showed no temperature dependence, at least in the temperature range of 2 degrees C-30 degrees C. The hump structure was successfully analyzed with a two-state worm-like chain model, and the Gibbs free energy difference of the detachment reaction was estimated to be 11.6 +/- 0.58 kcal/mol and found to be temperature independent. By contrast, upon lowering the temperature, the mean unfolding force from the partly unfolded intermediate state was found to markedly increase and the unfolding force distribution to broaden significantly, suggesting that the distance (x(u)) between the folded and transition states in the energy landscape along the pulling direction is decreased. These results suggest that the local structure of beta-strand A are stabilized by topologically simple local hydrogen-bond network and that the temperature does not affect the detachment reaction thermodynamically and kinetically, whereas the interaction between the beta-strands A' and G, which is a critical region for its mechanical stability, is strongly dependent on the temperature.
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35
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Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling. Proc Natl Acad Sci U S A 2008; 105:1204-8. [PMID: 18202182 DOI: 10.1073/pnas.0707500105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The force-extension profile of tetrameric spectrin is determined by using multiscale computer simulation. Fluctuation results of atomistic simulations of double spectrin repeat units (DSRU) are used to systematically build a coarse-grained (CG) model for the tetrameric form of spectrin. It is found that the spectrin tetramer can be modeled as a soft polymer with a unique flat force-extension profile over the range of biologically important lengths. It is also concluded that in the cytoskeletal network of the red blood cell the tetramer is in an "overcompressed" state. These findings are in contrast to the commonly used models of spectrin tetramer elasticity, namely the "entropic spring" polymer models. From these results, it is concluded that stable intact helical linker regions are needed to maintain the soft elasticity of the spectrin tetramer.
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36
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Cao Y, Li H. How Do Chemical Denaturants Affect the Mechanical Folding and Unfolding of Proteins? J Mol Biol 2008; 375:316-24. [DOI: 10.1016/j.jmb.2007.10.024] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 09/26/2007] [Accepted: 10/10/2007] [Indexed: 11/26/2022]
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37
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Paramore S, Ayton GS, Voth GA. Transient violations of the second law of thermodynamics in protein unfolding examined using synthetic atomic force microscopy and the fluctuation theorem. J Chem Phys 2007; 127:105105. [PMID: 17867784 DOI: 10.1063/1.2764487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The synthetic atomic force microscopy (AFM) method is developed to simulate a periodically replicated atomistic system subject to force and length fluctuations characteristic of an AFM experiment. This new method is used to examine the forced-extension and subsequent rupture of the alpha-helical linker connecting periodic images of a spectrin protein repeat unit. A two-dimensional potential of mean force (PMF) along the length and a reaction coordinate describing the state of the linker was calculated. This PMF reveals that the basic material properties of the spectrin repeat unit are sensitive to the state of linker, an important feature that cannot be accounted for in a one-dimensional PMF. Furthermore, nonequilibrium simulations were generated to examine the rupture event in the context of the fluctuation theorem. These atomistic simulations demonstrate that trajectories which are in apparent violation of the second law can overcome unfolding barriers at significantly reduced rupture forces.
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Affiliation(s)
- Sterling Paramore
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
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38
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Abstract
To identify cytoskeletal proteins that change conformation or assembly within stressed cells, in situ labeling of sterically shielded cysteines with fluorophores was analyzed by fluorescence imaging, quantitative mass spectrometry, and sequential two-dye labeling. Within red blood cells, shotgun labeling showed that shielded cysteines in the two isoforms of the cytoskeletal protein spectrin were increasingly labeled as a function of shear stress and time, indicative of forced unfolding of specific domains. Within mesenchymal stem cells-as a prototypical adherent cell-nonmuscle myosin IIA and vimentin are just two of the cytoskeletal proteins identified that show differential labeling in tensed versus drug-relaxed cells. Cysteine labeling of proteins within live cells can thus be used to fluorescently map out sites of molecular-scale deformation, and the results also suggest means to colocalize signaling events such as phosphorylation with forced unfolding.
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Affiliation(s)
- Colin P. Johnson
- Biophysical Engineering Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hsin-Yao Tang
- Systems Biology Division—The Wistar Institute, Philadelphia, PA 19104, USA
| | - Christine Carag
- Biophysical Engineering Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David W. Speicher
- Systems Biology Division—The Wistar Institute, Philadelphia, PA 19104, USA
| | - Dennis E. Discher
- Biophysical Engineering Lab, University of Pennsylvania, Philadelphia, PA 19104, USA
- Systems Biology Division—The Wistar Institute, Philadelphia, PA 19104, USA
- To whom correspondence should be addressed. E-mail:
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39
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Pu J, Ma S, Gao J, Truhlar DG. Small temperature dependence of the kinetic isotope effect for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase. J Phys Chem B 2007; 109:8551-6. [PMID: 16852008 PMCID: PMC4476250 DOI: 10.1021/jp051184c] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The H/D primary kinetic isotope effect (KIE) for the hydride transfer reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) is calculated as a function of temperature employing ensemble-averaged variational transition-state theory with multidimensional tunneling. The calculated KIEs display only a small temperature dependence over the temperature range of 5 to 45 degrees C. We identify two key features that contribute to canceling most of the temperature dependence of the KIE that would be expected on the basis of simpler models. Related issues such as the isotope effects on Arrhenius preexponential factors, large differences between free energies of activation and Arrhenius activation energy, and fluctuations of effective barriers are also discussed.
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Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431, USA
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40
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Spagnoli C, Beyder A, Besch SR, Sachs F. Drift-free atomic force microscopy measurements of cell height and mechanical properties. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2007; 78:036111. [PMID: 17411236 DOI: 10.1063/1.2534889] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Atomic force microscopy (AFM) is used to study the morphological and mechanical properties of living cells. However, experiments performed over minutes to hours are subject to significant instrumental drift. The main sources of drift are the cantilever's geometrical asymmetry and bimorphic construction. We developed a simple software Stick-and-Move (SaM) routine for AFM that eliminates drift by continuously referencing the sample position to the substrate while acquiring force-distance curves. Control experiments show no drift over 15 min at an acquisition rate of 0.1 Hz. As a proof of concept, we applied the SaM to study the response of rat astrocytes to osmotic stress, observing dimensional and constitutive changes during volume regulation.
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Affiliation(s)
- Chiara Spagnoli
- Department of Physiology and Biophysics, University at Buffalo, State University of New York, 3435 Main Street, 301 Cary Hall, Buffalo, NY 14214, USA
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41
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Forman JR, Clarke J. Mechanical unfolding of proteins: insights into biology, structure and folding. Curr Opin Struct Biol 2007; 17:58-66. [PMID: 17251000 DOI: 10.1016/j.sbi.2007.01.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 12/13/2006] [Accepted: 01/12/2007] [Indexed: 10/23/2022]
Abstract
Since user-friendly atomic force microscopes came onto the market a few years ago, scientists have explored the response of many proteins to applied force. This field has now matured beyond the phenomenological with exciting recent developments, particularly with regards to research into biological questions. For example, detailed mechanistic studies have suggested how mechanically active proteins perform their functions. Also, in vitro forced unfolding has been compared with in vivo protein import and degradation. Additionally, investigations have been carried out that probe the relationship between protein structure and response to applied force, an area that has benefited significantly from synergy between experiments and simulations. Finally, recent technological developments offer exciting new avenues for experimental studies.
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Affiliation(s)
- Julia R Forman
- Cambridge University Department of Chemistry, MRC Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK
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42
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An X, Zhang X, Salomao M, Guo X, Yang Y, Wu Y, Gratzer W, Baines AJ, Mohandas N. Thermal stabilities of brain spectrin and the constituent repeats of subunits. Biochemistry 2007; 45:13670-6. [PMID: 17087521 PMCID: PMC4401158 DOI: 10.1021/bi061368x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The different genes that encode mammalian spectrins give rise to proteins differing in their apparent stiffness. To explore this, we have compared the thermal stabilities of the structural repeats of brain spectrin subunits (alphaII and betaII) with those of erythrocyte spectrin (alphaI and betaI). The unfolding transition midpoints (T(m)) of the 36 alphaII- and betaII-spectrin repeats extend between 24 and 82 degrees C, with an average higher by some 10 degrees C than that of the alphaI- and betaI-spectrin repeats. This difference is reflected in the T(m) values of the intact brain and erythrocyte spectrins. Two of three tandem-repeat constructs from brain spectrin exhibited strong cooperative coupling, with elevation of the T(m) of the less stable partner corresponding to coupling free energies of approximately -4.4 and -3.5 kcal/mol. The third tandem-repeat construct, by contrast, exhibited negligible cooperativity. Tandem-repeat mutants, in which a part of the "linker" helix that connects the two domains was replaced with a corresponding helical segment from erythroid spectrin, showed only minor perturbation of the thermal melting profiles, without breakdown of cooperativity. Thus, the linker regions, which tolerate few point mutations without loss of cooperative function, have evidently evolved to permit conformational coupling in specified regions. The greater structural stability of the repeats in alphaII- and betaII-spectrin may account, at least in part, for the higher rigidity of brain compared to erythrocyte spectrin.
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Affiliation(s)
- Xiuli An
- Red Cell Physiology Laboratory, New York Blood Center, New York, New York 10021, USA.
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43
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Randles LG, Rounsevell RWS, Clarke J. Spectrin domains lose cooperativity in forced unfolding. Biophys J 2007; 92:571-7. [PMID: 17085494 PMCID: PMC1751415 DOI: 10.1529/biophysj.106.093690] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 10/10/2006] [Indexed: 11/18/2022] Open
Abstract
Spectrin is a multidomain cytoskeletal protein, the component three-helix bundle domains are expected to experience mechanical force in vivo. In thermodynamic and kinetic studies, neighboring domains of chicken brain alpha-spectrin R16 and R17 have been shown to behave cooperatively. Is this cooperativity maintained under force? The effect of force on these spectrin domains was investigated using atomic force microscopy. The response of the individual domains to force was compared to that of the tandem repeat R1617. Importantly, nonhelical linkers (all-beta immunoglobulin domains) were used to avoid formation of nonnative helical linkers. We show that, in contrast to previous studies on spectrin repeats, only 3% of R1617 unfolding events gave an increase in contour length consistent with cooperative two-domain unfolding events. Furthermore, the unfolding forces for R1617 were the same as those for the unfolding of R16 or R17 alone. This is a strong indication that the cooperative unfolding behavior observed in the stopped-flow studies is absent between these spectrin domains when force is acting as a denaturant. Our evidence suggests that the rare double unfolding events result from misfolding between adjacent repeats. We suggest that this switch from cooperative to independent behavior allows multidomain proteins to maintain integrity under applied force.
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Affiliation(s)
- Lucy G Randles
- Department of Chemistry, University of Cambridge, MRC Centre for Protein Engineering, Cambridge, United Kingdom
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44
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Johnson CP, Gaetani M, Ortiz V, Bhasin N, Harper S, Gallagher PG, Speicher DW, Discher DE. Pathogenic proline mutation in the linker between spectrin repeats: disease caused by spectrin unfolding. Blood 2006; 109:3538-43. [PMID: 17192394 PMCID: PMC1852230 DOI: 10.1182/blood-2006-07-038588] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic mutations in alpha and beta spectrin result in a variety of syndromes, including hereditary elliptocytosis (HE), hereditary pyropoikilocytosis (HPP), and hereditary spherocytosis (HS). Although some mutations clearly lie at sites of interaction, such as the sites of spectrin alpha-betatetramer formation, a surprising number of HE-causing mutations have been identified within linker regions between distal spectrin repeats. Here we apply solution structural and single molecule methods to the folding and stability of recombinant proteins consisting of the first 5 spectrin repeats of alpha-spectrin, comparing normal spectrin with a pathogenic linker mutation, Q471P, between repeats R4 and R5. Results show that the linker mutation destabilizes a significant fraction of the 5-repeat construct at 37 degrees C, whereas the WT remains fully folded well above body temperature. In WT protein, helical linkers propagate stability from one repeat to the next, but the mutation disrupts the stabilizing influence of adjacent repeats. The results suggest a molecular mechanism for the high frequency of disease caused by proline mutations in spectrin linkers.
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Affiliation(s)
- Colin P Johnson
- Molecular and Cell Biophysics Laboratory, University of Pennsylvania, 3699 Market Street, Philadelphia, PA 19104, USA
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45
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An X, Salomao M, Guo X, Gratzer W, Mohandas N. Tropomyosin modulates erythrocyte membrane stability. Blood 2006; 109:1284-8. [PMID: 17008534 PMCID: PMC1785134 DOI: 10.1182/blood-2006-07-036954] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ternary complex of spectrin, actin, and 4.1R (human erythrocyte protein 4.1) defines the nodes of the erythrocyte membrane skeletal network and is inseparable from membrane stability under mechanical stress. These junctions also contain tropomyosin (TM) and the other actin-binding proteins, adducin, protein 4.9, tropomodulin, and a small proportion of capZ, the functions of which are poorly defined. Here, we have examined the consequences of selective elimination of TM from the membrane. We have shown that the mechanical stability of the membranes of resealed ghosts devoid of TM is grossly, but reversibly, impaired. That the decreased membrane stability of TM-depleted membranes is the result of destabilization of the ternary complex of the network junctions is demonstrated by the strongly facilitated entry into the junctions in situ of a beta-spectrin peptide, containing the actin- and 4.1R-binding sites, after extraction of the TM. The stabilizing effect of TM is highly specific, in that it is only the endogenous isotype, and not the slightly longer muscle TM that can bind to the depleted membranes and restore their mechanical stability. These findings have enabled us identify a function for TM in elevating the mechanical stability of erythrocyte membranes by stabilizing the spectrin-actin-4.1R junctional complex.
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Affiliation(s)
- Xiuli An
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY 10021, USA.
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46
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Ritort F. Single-molecule experiments in biological physics: methods and applications. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2006; 18:R531-R583. [PMID: 21690856 DOI: 10.1088/0953-8984/18/32/r01] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
I review single-molecule experiments (SMEs) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SMEs it is possible to manipulate molecules one at a time and measure distributions describing molecular properties, characterize the kinetics of biomolecular reactions and detect molecular intermediates. SMEs provide additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SMEs it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level, emphasizing the importance of SMEs to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SMEs from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOTs), magnetic tweezers (MTs), biomembrane force probes (BFPs) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation) and proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SMEs to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.
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Affiliation(s)
- F Ritort
- Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
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47
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Paramore S, Voth GA. Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules. Biophys J 2006; 91:3436-45. [PMID: 16891371 PMCID: PMC1614492 DOI: 10.1529/biophysj.106.091108] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unfolding pathways of multiple-repeat spectrin molecules were examined using steered molecular dynamics (SMD) simulations to forcibly unfold double- and triple-repeat spectrin molecules. Although SMD has previously been used to study other repeating-domain proteins, spectrin offers a unique challenge in that the linker connecting repeat units has a definite secondary structure, that of an alpha-helix. Therefore, the boundary conditions imposed on a double- or triple-repeat spectrin must be carefully considered if any relationship to the real system is to be deduced. This was accomplished by imposing additional forces on the system which ensure that the terminal alpha-helices behave as if there were no free noncontiguous helical ends. The results of the SMD simulations highlight the importance of the rupture of the alpha-helical linker on the subsequent unfolding events. Rupture of the linker propagates unfolding in the adjacent repeat units by destabilizing the tertiary structure, ultimately resulting in complete unfolding of the affected repeat unit. Two dominant classes of unfolding pathways are observed after the initial rupture of a linker which involve either rupture of another linker (possibly adjacent) or rupture of the basic tertiary structure of a repeat unit. The relationship between the force response observed on simulation timescales and those of experiment or physiological conditions is also discussed.
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Affiliation(s)
- Sterling Paramore
- Department of Chemistry, Center for Biophysical Modeling and Simulation, University of Utah, Salt Lake City, 84112-0850, USA
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48
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Discher DE, Bhasin N, Johnson CP. Covalent chemistry on distended proteins. Proc Natl Acad Sci U S A 2006; 103:7533-4. [PMID: 16682625 PMCID: PMC1472479 DOI: 10.1073/pnas.0602388103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dennis E Discher
- Molecular and Cell Biophysics Laboratory and Nano/Bio Interface Center, University of Pennsylvania, Philadelphia, PA 19104, USA.
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49
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Cieplak M, Filipek S, Janovjak H, Krzyśko KA. Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:537-44. [PMID: 16678120 DOI: 10.1016/j.bbamem.2006.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Revised: 03/11/2006] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard-Jones contact interactions is applied to model the protein-membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins.
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Affiliation(s)
- Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
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50
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An X, Guo X, Zhang X, Baines AJ, Debnath G, Moyo D, Salomao M, Bhasin N, Johnson C, Discher D, Gratzer WB, Mohandas N. Conformational Stabilities of the Structural Repeats of Erythroid Spectrin and Their Functional Implications. J Biol Chem 2006; 281:10527-32. [PMID: 16476728 DOI: 10.1074/jbc.m513725200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The two polypeptide chains of the erythroid spectrin heterodimer contain between them 36 structural repeating modules, which can function as independently folding units. We have expressed all 36 and determined their thermal stabilities. These vary widely, with unfolding transition mid-points (T(m)) ranging from 21 to 72 degrees C. Eight of the isolated repeats are largely unfolded at physiological temperature. Constructs comprising two or more adjacent repeats show inter-repeat coupling with coupling free energies of several kcal mol(-1). Constructs comprising five successive repeats from the beta-chain displayed cooperativity and strong temperature dependence in forced unfolding by atomic force microscopy. Analysis of aligned sequences and molecular modeling suggests that high stability is conferred by large hydrophobic side chains at position e of the heptad hydrophobic repeats in the first helix of the three-helix bundle that makes up each repeat. This inference was borne out by the properties of mutants in which the critical residues have been replaced. The marginal stability of the tertiary structure at several points in the spectrin chains is moderated by energetic coupling with adjoining structural elements but may be expected to permit adaptation of the membrane to the large distortions that the red cell experiences in the circulation.
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Affiliation(s)
- Xiuli An
- Red Cell Physiology Laboratory, New York Blood Center, 310 E. 67th Street, New York, NY 10021, USA.
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