1
|
Sloas DC, Tran JC, Marzilli AM, Ngo JT. Tension-tuned receptors for synthetic mechanotransduction and intercellular force detection. Nat Biotechnol 2023; 41:1287-1295. [PMID: 36646932 PMCID: PMC10499187 DOI: 10.1038/s41587-022-01638-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/08/2022] [Indexed: 01/18/2023]
Abstract
Cells interpret mechanical stimuli from their environments and neighbors, but the ability to engineer customized mechanosensing capabilities has remained a synthetic and mechanobiology challenge. Here we introduce tension-tuned synthetic Notch (SynNotch) receptors to convert extracellular and intercellular forces into specifiable gene expression changes. By elevating the tension requirements of SynNotch activation, in combination with structure-guided mutagenesis, we designed a set of receptors with mechanical sensitivities spanning the physiologically relevant picoNewton range. Cells expressing these receptors can distinguish between varying tensile forces and respond by enacting customizable transcriptional programs. We applied these tools to design a decision-making circuit, through which fibroblasts differentiate into myoblasts upon stimulation with distinct tension magnitudes. We also characterize cell-generated forces transmitted between cells during Notch signaling. Overall, this work provides insight into how mechanically induced changes in protein structure can be used to transduce physical forces into biochemical signals. The system should facilitate the further programming and dissection of force-related phenomena in biological systems.
Collapse
Affiliation(s)
- D Christopher Sloas
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - Jeremy C Tran
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - Alexander M Marzilli
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA
| | - John T Ngo
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, USA.
| |
Collapse
|
2
|
Anderson DM, Jayanthi LP, Gosavi S, Meiering EM. Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity. Front Mol Biosci 2023; 10:1021733. [PMID: 36845544 PMCID: PMC9945329 DOI: 10.3389/fmolb.2023.1021733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.
Collapse
Affiliation(s)
| | - Lakshmi P. Jayanthi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Elizabeth M. Meiering
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada,*Correspondence: Elizabeth M. Meiering,
| |
Collapse
|
3
|
Beedle AEM, Garcia-Manyes S. The role of single protein elasticity in mechanobiology. NATURE REVIEWS. MATERIALS 2023; 8:10-24. [PMID: 37469679 PMCID: PMC7614781 DOI: 10.1038/s41578-022-00488-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 07/21/2023]
Abstract
In addition to biochemical signals and genetic considerations, mechanical forces are rapidly emerging as a master regulator of human physiology. Yet the molecular mechanisms that regulate force-induced functionalities across a wide range of scales, encompassing the cell, tissue or organ levels, are comparatively not so well understood. With the advent, development and refining of single molecule nanomechanical techniques, enabling to exquisitely probe the conformational dynamics of individual proteins under the effect of a calibrated force, we have begun to acquire a comprehensive knowledge on the rich plethora of physicochemical principles that regulate the elasticity of single proteins. Here we review the major advances underpinning our current understanding of how the elasticity of single proteins regulates mechanosensing and mechanotransduction. We discuss the present limitations and future challenges of such a prolific and burgeoning field.
Collapse
Affiliation(s)
- Amy EM Beedle
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
| |
Collapse
|
4
|
Ferenczy GG, Kellermayer M. Contribution of Hydrophobic Interactions to Protein Mechanical Stability. Comput Struct Biotechnol J 2022; 20:1946-1956. [PMID: 35521554 PMCID: PMC9062142 DOI: 10.1016/j.csbj.2022.04.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/07/2022] [Accepted: 04/17/2022] [Indexed: 11/26/2022] Open
Abstract
The role of hydrophobic and polar interactions in providing thermodynamic stability to folded proteins has been intensively studied, but the relative contribution of these interactions to the mechanical stability is less explored. We used steered molecular dynamics simulations with constant-velocity pulling to generate force-extension curves of selected protein domains and monitor hydrophobic surface unravelling upon extension. Hydrophobic contribution was found to vary between one fifth and one third of the total force while the rest of the contribution is attributed primarily to hydrogen bonds. Moreover, hydrophobic force peaks were shifted towards larger protein extensions with respect to the force peaks attributed to hydrogen bonds. The higher importance of hydrogen bonds compared to hydrophobic interactions in providing mechanical resistance is in contrast with the relative importance of the hydrophobic interactions in providing thermodynamic stability of proteins. The different contributions of these interactions to the mechanical stability are explained by the steeper free energy dependence of hydrogen bonds compared to hydrophobic interactions on the relative positions of interacting atoms. Comparative analyses for several protein domains revealed that the variation of hydrophobic forces is modest, while the contribution of hydrogen bonds to the force peaks becomes increasingly important for mechanically resistant protein domains.
Collapse
|
5
|
Perišić O, Wriggers W. Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis. Front Mol Biosci 2021; 8:696609. [PMID: 34660691 PMCID: PMC8516001 DOI: 10.3389/fmolb.2021.696609] [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: 04/17/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
We employed mutual information (MI) analysis to detect motions affecting the mechanical resistance of the human-engineered protein Top7. The results are based on the MI analysis of pair contact correlations measured in steered molecular dynamics (SMD) trajectories and their statistical dependence on global unfolding. This study is the first application of the MI analysis to SMD forced unfolding, and we furnish specific SMD recommendations for the utility of parameters and options in the TimeScapes package. The MI analysis provided a global overview of the effect of perturbation on the stability of the protein. We also employed a more conventional trajectory analysis for a detailed description of the mechanical resistance of Top7. Specifically, we investigated 1) the hydropathy of the interactions of structural segments, 2) the H2O concentration near residues relevant for unfolding, and 3) the changing hydrogen bonding patterns and main chain dihedral angles. The results show that the application of MI in the study of protein mechanical resistance can be useful for the engineering of more resistant mutants when combined with conventional analysis. We propose a novel mutation design based on the hydropathy of residues that would stabilize the unfolding region by mimicking its more stable symmetry mate. The proposed design process does not involve the introduction of covalent crosslinks, so it has the potential to preserve the conformational space and unfolding pathway of the protein.
Collapse
Affiliation(s)
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, United States
| |
Collapse
|
6
|
Li H. There Is Plenty of Room in The Folded Globular Proteins: Tandem Modular Elastomeric Proteins Offer New Opportunities in Engineering Protein‐Based Biomaterials. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Hongbin Li
- Department of Chemistry University of British Columbia Vancouver BC V6T 1Z1 Canada
| |
Collapse
|
7
|
Chandler PG, Buckle AM. Development and Differentiation in Monobodies Based on the Fibronectin Type 3 Domain. Cells 2020; 9:E610. [PMID: 32143310 PMCID: PMC7140400 DOI: 10.3390/cells9030610] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 12/13/2022] Open
Abstract
As a non-antibody scaffold, monobodies based on the fibronectin type III (FN3) domain overcome antibody size and complexity while maintaining analogous binding loops. However, antibodies and their derivatives remain the gold standard for the design of new therapeutics. In response, clinical-stage therapeutic proteins based on the FN3 domain are beginning to use native fibronectin function as a point of differentiation. The small and simple structure of monomeric monobodies confers increased tissue distribution and reduced half-life, whilst the absence of disulphide bonds improves stability in cytosolic environments. Where multi-specificity is challenging with an antibody format that is prone to mis-pairing between chains, multiple FN3 domains in the fibronectin assembly already interact with a large number of molecules. As such, multiple monobodies engineered for interaction with therapeutic targets are being combined in a similar beads-on-a-string assembly which improves both efficacy and pharmacokinetics. Furthermore, full length fibronectin is able to fold into multiple conformations as part of its natural function and a greater understanding of how mechanical forces allow for the transition between states will lead to advanced applications that truly differentiate the FN3 domain as a therapeutic scaffold.
Collapse
Affiliation(s)
- Peter G. Chandler
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Australia;
| | | |
Collapse
|
8
|
Xia J, Zuo J, Li H. Single molecule force spectroscopy reveals that the oxidation state of cobalt ions plays an important role in enhancing the mechanical stability of proteins. NANOSCALE 2019; 11:19791-19796. [PMID: 31612899 DOI: 10.1039/c9nr06912g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Engineered bi-histidine (biHis)-based metal chelation is a general and robust method to enhance the mechanical stability of proteins. Here we used single molecule force spectroscopy techniques to investigate the effect of binding of Co2+/Co3+ on the mechanical stability of an engineered biHis mutant of protein GB1, G6-53. We found that the binding of Co2+/Co3+ can lead to an enhancement of the mechanical stability of G6-53, but the degree of enhancement is drastically different. The binding of Co2+ can only lead to marginal enhancement of G6-53's mechanical stability, while Co3+ has a much stronger effect. This large difference is likely due to the large difference in thermodynamic stability and kinetic lability of Co2+ and Co3+ complexes. These results opened up new avenues towards fine tuning the mechanical properties of proteins.
Collapse
Affiliation(s)
- Jiahao Xia
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada. and Key Laboratory of Organic Optoelectronic and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 10084, P. R. China
| | - Jiacheng Zuo
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Jemima Beulin DS, Ponnuraj K. Steered molecular dynamics study reveals insights into the function of the repetitive B region of collagen- and fibrinogen-binding MSCRAMMs. J Biomol Struct Dyn 2016; 35:535-550. [PMID: 26861150 DOI: 10.1080/07391102.2016.1152566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) are modular proteins covalently anchored in the bacterial cell wall of many Gram-positive bacteria. The N-terminal region of most MSCRAMMs carries the ligand-binding domains (A region) which specifically target the host extracellular matrix (ECM) proteins such as collagen, fibrinogen and fibronectin. In Staphylococcus aureus Cna, the prototype collagen-binding MSCRAMM, the A region is followed by a repetitive B region which is found to be conserved among many Gram-positive bacteria. This conservation signifies an important functional role for the B region which is made of repetitive domains. It was suggested that this region could act as a 'stalk' as well as a 'spring' to present the ligand-binding A region, away from the bacterial surface. But there is no clear functional implication of this region available till date. Each repetitive domain in the B region possesses a variant of the Ig fold called the CnaB fold. Additionally, the B repeats are also paired and the pairs are clustered together. To investigate if the B domains have a function similar to the Ig domains in the I-band region of the giant muscle protein, titin, steered molecular dynamics simulations of one, two and four B repeats of Cna were carried out. The results of the simulations suggest that the B region could provide mechanical stability, extensibility and elasticity to Cna due to the CnaB fold as well as the clustered arrangement of their domains. This study thus provided further insights into the biological underpinnings of adhesin-host interaction.
Collapse
Affiliation(s)
- D S Jemima Beulin
- a Centre of Advanced Study in Crystallography and Biophysics , University of Madras , Guindy Campus, Chennai 600 025 , India
| | - Karthe Ponnuraj
- a Centre of Advanced Study in Crystallography and Biophysics , University of Madras , Guindy Campus, Chennai 600 025 , India
| |
Collapse
|
11
|
Oroz J, Bruix M, Laurents D, Galera-Prat A, Schönfelder J, Cañada F, Carrión-Vázquez M. The Y9P Variant of the Titin I27 Module: Structural Determinants of Its Revisited Nanomechanics. Structure 2016; 24:606-616. [DOI: 10.1016/j.str.2016.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/30/2015] [Accepted: 02/22/2016] [Indexed: 11/28/2022]
|
12
|
Tych KM, Batchelor M, Hoffmann T, Wilson MC, Paci E, Brockwell DJ, Dougan L. Tuning protein mechanics through an ionic cluster graft from an extremophilic protein. SOFT MATTER 2016; 12:2688-2699. [PMID: 26809452 DOI: 10.1039/c5sm02938d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteins from extremophilic organisms provide excellent model systems to determine the role of non-covalent interactions in defining protein stability and dynamics as well as being attractive targets for the development of robust biomaterials. Hyperthermophilic proteins have a prevalence of salt bridges, relative to their mesophilic homologues, which are thought to be important for enhanced thermal stability. However, the impact of salt bridges on the mechanical properties of proteins is far from understood. Here, a combination of protein engineering, biophysical characterisation, single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations directly investigates the role of salt bridges in the mechanical stability of two cold shock proteins; BsCSP from the mesophilic organism Bacillus subtilis and TmCSP from the hyperthermophilic organism Thermotoga maritima. Single molecule force spectroscopy shows that at ambient temperatures TmCSP is mechanically stronger yet, counter-intuitively, its native state can withstand greater deformation before unfolding (i.e. it is mechanically soft) compared with BsCSP. MD simulations were used to identify the location and quantify the population of salt bridges, and reveal that TmCSP contains a larger number of highly occupied salt bridges than BsCSP. To test the hypothesis that salt-bridges endow these mechanical properties on the hyperthermophilic CSP, a charged triple mutant (CTM) variant of BsCSP was generated by grafting an ionic cluster from TmCSP into the BsCSP scaffold. As expected CTM is thermodynamically more stable and mechanically softer than BsCSP. We show that a grafted ionic cluster can increase the mechanical softness of a protein and speculate that it could provide a mechanical recovery mechanism and that it may be a design feature applicable to other proteins.
Collapse
Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
| | | | | | | | | | | | | |
Collapse
|
13
|
Life in extreme environments: single molecule force spectroscopy as a tool to explore proteins from extremophilic organisms. Biochem Soc Trans 2015; 43:179-85. [DOI: 10.1042/bst20140274] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Extremophiles are organisms which survive and thrive in extreme environments. The proteins from extremophilic single-celled organisms have received considerable attention as they are structurally stable and functionally active under extreme physical and chemical conditions. In this short article, we provide an introduction to extremophiles, the structural adaptations of proteins from extremophilic organisms and the exploitation of these proteins in industrial applications. We provide a review of recent developments which have utilized single molecule force spectroscopy to mechanically manipulate proteins from extremophilic organisms and the information which has been gained about their stability, flexibility and underlying energy landscapes.
Collapse
|
14
|
|
15
|
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
|
16
|
Trudeau DL, Smith MA, Arnold FH. Innovation by homologous recombination. Curr Opin Chem Biol 2013; 17:902-9. [DOI: 10.1016/j.cbpa.2013.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 10/03/2013] [Indexed: 12/11/2022]
|
17
|
A novel approach for protein subcellular location prediction using amino acid exposure. BMC Bioinformatics 2013; 14:342. [PMID: 24283794 PMCID: PMC4219330 DOI: 10.1186/1471-2105-14-342] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/25/2013] [Indexed: 11/10/2022] Open
Abstract
Background Proteins perform their functions in associated cellular locations. Therefore, the study of protein function can be facilitated by predictions of protein location. Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. Here we expand this approach taking into account amino acid composition at different levels of amino acid exposure. Results Our method has two stages. For stage one, we trained multiple Support Vector Machines (SVMs) to score eukaryotic protein sequences for membership to each of three categories: nuclear, cytoplasmic and extracellular, plus extra category nucleocytoplasmic, accounting for the fact that a large number of proteins shuttles between those two locations. In stage two we use an artificial neural network (ANN) to propose a category from the scores given to the four locations in stage one. The method reaches an accuracy of 68% when using as input 3D-derived values of amino acid exposure. Calibration of the method using predicted values of amino acid exposure allows classifying proteins without 3D-information with an accuracy of 62% and discerning proteins in different locations even if they shared high levels of identity. Conclusions In this study we explored the relationship between residue exposure and protein subcellular location. We developed a new algorithm for subcellular location prediction that uses residue exposure signatures. Our algorithm uses a novel approach to address the multiclass classification problem. The algorithm is implemented as web server 'NYCE’ and can be accessed at http://cbdm.mdc-berlin.de/~amer/nyce.
Collapse
|
18
|
Li YD, Lamour G, Gsponer J, Zheng P, Li H. The molecular mechanism underlying mechanical anisotropy of the protein GB1. Biophys J 2013; 103:2361-8. [PMID: 23283235 DOI: 10.1016/j.bpj.2012.10.035] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/19/2012] [Accepted: 10/26/2012] [Indexed: 10/27/2022] Open
Abstract
Mechanical responses of elastic proteins are crucial for their biological function and nanotechnological use. Loading direction has been identified as one key determinant for the mechanical responses of proteins. However, it is not clear how a change in pulling direction changes the mechanical unfolding mechanism of the protein. Here, we combine protein engineering, single-molecule force spectroscopy, and steered molecular dynamics simulations to systematically investigate the mechanical response of a small globular protein GB1. Force versus extension profiles from both experiments and simulations reveal marked mechanical anisotropy of GB1. Using native contact analysis, we relate the mechanically robust shearing geometry with concurrent rupture of native contacts. This clearly contrasts the sequential rupture observed in simulations for the mechanically labile peeling geometry. Moreover, we identify multiple distinct mechanical unfolding pathways in two loading directions. Implications of such diverse unfolding mechanisms are discussed. Our results may also provide some insights for designing elastomeric proteins with tailored mechanical properties.
Collapse
Affiliation(s)
- Yongnan Devin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | | | | |
Collapse
|
19
|
Sasaki M, Inoue M, Katada Y, Taguchi T. Promotion of initial cell adhesion on trisuccinimidyl citrate-modified nickel-free high-nitrogen stainless steel. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2013; 24:951-958. [PMID: 23334307 DOI: 10.1007/s10856-012-4845-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/20/2012] [Indexed: 06/01/2023]
Abstract
The surface of nickel-free high-nitrogen stainless steel (HNS) was modified with a citric acid-based cross-linker, trisuccinimidyl citrate (TSC), to promote initial cell adhesion in external skeletal fixation pins. The remaining active ester groups on TSC-immobilized HNS reacted with the amino groups of serum proteins. The immobilized serum proteins formed cell recognition sites to promote the initial cell adhesion immediately after cell seeding. The amount of fibronectin, which is a typical cell adhesion protein, immobilized on the TSC-immobilized HNS surface was threefold greater than on the original HNS after only 15 min. The fibroblastic cell culture experiments showed that the initial cell adhesion was significantly enhanced on the TSC-immobilized HNS compared with the original HNS at 3 h. Furthermore, the cell adhesion activity of the TSC-immobilized HNS continued to promote cell proliferation even at 7 days. Therefore, TSC-immobilized HNS may enable the rapid integration of soft tissues through its reaction with the patient's serum proteins and extracellular proteins around the surgical site.
Collapse
Affiliation(s)
- Makoto Sasaki
- Graduate School of Pure and Applied Science, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | | | | |
Collapse
|
20
|
Hoffmann T, Tych KM, Brockwell DJ, Dougan L. Single-molecule force spectroscopy identifies a small cold shock protein as being mechanically robust. J Phys Chem B 2013; 117:1819-26. [PMID: 23293964 DOI: 10.1021/jp310442s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Single-molecule force spectroscopy has emerged as a powerful approach to examine the stability and dynamics of single proteins. We have completed force extension experiments on the small cold shock protein B from Thermotoga maritima, using a specially constructed chimeric polyprotein. The protein's simple topology, which is distinct from the mechanically well-characterized β-grasp and immunoglobulin (Ig)-like folds, in addition to the wide range of structural homologues resulting from its ancient origin, provides an attractive model protein for single-molecule force spectroscopy studies. We have determined that the protein has mechanical stability, unfolding at greater than 70 pN at a pulling velocity of 100 nm s(-1). We reveal features of the unfolding energy landscape by measuring the dependence of the mechanical stability on pulling velocity, in combination with Monte Carlo simulations. We show that the cold shock protein has mechanically robust, yet malleable, features that may be important in providing the protein with stability and flexibility to function over a range of environmental conditions. These results provide insights into the relationship between the secondary structure and topology of a protein and its mechanical strength. This lays the foundation for the investigation of the effects of changes in environmental conditions on the mechanical and dynamic properties of cold shock proteins.
Collapse
Affiliation(s)
- Toni Hoffmann
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | | | | | | |
Collapse
|
21
|
Hoffmann T, Tych KM, Hughes ML, Brockwell DJ, Dougan L. Towards design principles for determining the mechanical stability of proteins. Phys Chem Chem Phys 2013; 15:15767-80. [DOI: 10.1039/c3cp52142g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
22
|
Affiliation(s)
- Elias M. Puchner
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158;
| | - Hermann E. Gaub
- Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany;
| |
Collapse
|
23
|
Fang J, Li H. A facile way to tune mechanical properties of artificial elastomeric proteins-based hydrogels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8260-8265. [PMID: 22554148 DOI: 10.1021/la301225w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Protein-based hydrogels have attracted considerable interests due to their potential applications in biomedical engineering and material sciences. Using a tandem modular protein (GB1)(8) as building blocks, we have engineered chemically cross-linked hydrogels via a photochemical cross-linking strategy, which is based on the cross-linking of two adjacent tyrosine residues into dityrosine adducts. However, because of the relatively low reactivity of tyrosine residues in GB1, (GB1)(8)-based hydrogels exhibit poor mechanical properties. Here, we report a Bolton-Hunter reagent-based, facile method to improve and tune the mechanical properties of such protein-based hydrogels. Using Bolton-Hunter reagent, we can derivatize lysine residues with phenolic functional groups to modulate the phenolic (tyrosine-like) content of (GB1)(8). We show that hydrogels made from derivatized (GB1)(8) with increased phenolic content show significantly improved mechanical properties, including improved Young's modulus, breaking modulus as well as reduced swelling. These results demonstrate the great potential of this derivatization method in constructing protein-based biomaterials with desired macroscopic mechanical properties.
Collapse
Affiliation(s)
- Jie Fang
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | | |
Collapse
|
24
|
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
|
25
|
Lu W, Negi SS, Oberhauser AF, Braun W. Engineering proteins with enhanced mechanical stability by force-specific sequence motifs. Proteins 2012; 80:1308-15. [PMID: 22274941 DOI: 10.1002/prot.24027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 12/22/2011] [Accepted: 01/02/2012] [Indexed: 11/09/2022]
Abstract
Use of atomic force microscopy (AFM) has recently led to a better understanding of the molecular mechanisms of the unfolding process by mechanical forces; however, the rational design of novel proteins with specific mechanical strength remains challenging. We have approached this problem from a new perspective that generates linear physical-chemical properties (PCP) motifs from a limited AFM data set. Guided by our linear sequence analysis, we designed and analyzed four new mutants of the titin I1 domain with the goal of increasing the domain's mechanical strength. All four mutants could be cloned and expressed as soluble proteins. AFM data indicate that at least two of the mutants have increased molecular mechanical strength. This observation suggests that the PCP method is useful to graft sequences specific for high mechanical stability to weak proteins to increase their mechanical stability, and represents an additional tool in the design of novel proteins besides steered molecular dynamics calculations, coarse grained simulations, and ϕ-value analysis of the transition state.
Collapse
Affiliation(s)
- Wenzhe Lu
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0857, USA
| | | | | | | |
Collapse
|
26
|
Bradshaw MJ, Smith ML. Contribution of unfolding and intermolecular architecture to fibronectin fiber extensibility. Biophys J 2012; 101:1740-8. [PMID: 21961600 DOI: 10.1016/j.bpj.2011.08.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 08/13/2011] [Accepted: 08/18/2011] [Indexed: 10/17/2022] Open
Abstract
The extracellular matrix contains components with remarkable mechanical properties, including fibronectin (Fn) fibers with extensibilities of >700% strain. We utilized what we consider a novel technique to quantify the extent of molecular unfolding that contributes to Fn fiber extension, and we compared this behavior with stochastic models of Fn fibers with different molecular arrangements. In vitro unfolding as a function of strain was measured by fluorescently labeling cysteines in modules FnIII7 and III15 in artificial Fn fibers. A calibration technique we also consider novel made it possible to demonstrate that 44% of cysteines in these modules were exposed in Fn fibers strained to 421% extension, up from 8% exposure without strain. In silico unfolding was measured by applying a constant strain rate to a fiber represented by a network of wormlike chain springs, each representing an individual Fn molecule. Unfolding rates were calculated with a tension-dependent stochastic model applied to FnIII modules in each molecule. A comparison of these approaches revealed that only a molecular arrangement permitting unequal mechanical loading of Fn molecules recapitulates in vitro unfolding. These data have implications for Fn-dependent mechanotransduction and give insight into how the molecular architecture of natural materials permits such remarkable extensibility.
Collapse
Affiliation(s)
- Mark J Bradshaw
- Department of Mechanical Engineering, Boston University, Boston, Massachusetts, USA
| | | |
Collapse
|
27
|
Free Energy Landscapes of Proteins: Insights from Mechanical Probes. ADVANCES IN CHEMICAL PHYSICS 2011. [DOI: 10.1002/9781118131374.ch14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
|
28
|
Enhancing the mechanical stability of proteins through a cocktail approach. Biophys J 2011; 100:1794-9. [PMID: 21463593 DOI: 10.1016/j.bpj.2011.02.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Revised: 01/23/2011] [Accepted: 02/14/2011] [Indexed: 11/22/2022] Open
Abstract
Rationally enhancing the mechanical stability of proteins remains a challenge in the field of single molecule force spectroscopy. Here we demonstrate that it is feasible to use a "cocktail" approach for combining more than one approach to enhance significantly the mechanical stability of proteins in an additive fashion. As a proof of principle, we show that metal chelation and protein-protein interaction can be combined to enhance the unfolding force of a protein to ∼450 pN, which is >3 times of its original value. This is also higher than the mechanical stability of most of proteins studied so far. We also extend such a cocktail concept to combine two different metal chelation sites to enhance protein mechanical stability. This approach opens new avenues to efficiently regulating the mechanical properties of proteins, and should be applicable to a wide range of elastomeric proteins.
Collapse
|
29
|
Li H, Cao Y. Protein mechanics: from single molecules to functional biomaterials. Acc Chem Res 2010; 43:1331-41. [PMID: 20669937 DOI: 10.1021/ar100057a] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Elastomeric proteins act as the essential functional units in a wide variety of biomechanical machinery and serve as the basic building blocks for biological materials that exhibit superb mechanical properties. These proteins provide the desired elasticity, mechanical strength, resilience, and toughness within these materials. Understanding the mechanical properties of elastomeric protein-based biomaterials is a multiscale problem spanning from the atomistic/molecular level to the macroscopic level. Uncovering the design principles of individual elastomeric building blocks is critical both for the scientific understanding of multiscale mechanics of biomaterials and for the rational engineering of novel biomaterials with desirable mechanical properties. The development of single-molecule force spectroscopy techniques has provided methods for characterizing mechanical properties of elastomeric proteins one molecule at a time. Single-molecule atomic force microscopy (AFM) is uniquely suited to this purpose. Molecular dynamic simulations, protein engineering techniques, and single-molecule AFM study have collectively revealed tremendous insights into the molecular design of single elastomeric proteins, which can guide the design and engineering of elastomeric proteins with tailored mechanical properties. Researchers are focusing experimental efforts toward engineering artificial elastomeric proteins with mechanical properties that mimic or even surpass those of natural elastomeric proteins. In this Account, we summarize our recent experimental efforts to engineer novel artificial elastomeric proteins and develop general and rational methodologies to tune the nanomechanical properties of elastomeric proteins at the single-molecule level. We focus on general design principles used for enhancing the mechanical stability of proteins. These principles include the development of metal-chelation-based general methodology, strategies to control the unfolding hierarchy of multidomain elastomeric proteins, and the design of novel elastomeric proteins that exhibit stimuli-responsive mechanical properties. Moving forward, we are now exploring the use of these artificial elastomeric proteins as building blocks of protein-based biomaterials. Ultimately, we would like to rationally tailor mechanical properties of elastomeric protein-based materials by programming the molecular sequence, and thus nanomechanical properties, of elastomeric proteins at the single-molecule level. This step would help bridge the gap between single protein mechanics and material biomechanics, revealing how the mechanical properties of individual elastomeric proteins are translated into the properties of macroscopic materials.
Collapse
Affiliation(s)
- Hongbin Li
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1 Canada
| | - Yi Cao
- Department of Chemistry, The University of British Columbia, Vancouver, BC V6T 1Z1 Canada
| |
Collapse
|
30
|
Magnusson JP, Bersani S, Salmaso S, Alexander C, Caliceti P. In situ growth of side-chain PEG polymers from functionalized human growth hormone-a new technique for preparation of enhanced protein-polymer conjugates. Bioconjug Chem 2010; 21:671-8. [PMID: 20201488 DOI: 10.1021/bc900468v] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The application of atom transfer radical polymerization (ATRP) for preparation of a novel class of protein-polymer bioconjugates is described, exemplified by the synthesis of a recombinant human growth hormone (rh-GH) poly(ethylene glycol) methyl ether methacrylate (PEGMA) hybrid. The rh-GH protein was activated via a bromo-ester functionalized linker and used as a macroinitiator to polymerize the hydrophilic monomer PEGMA under solely aqueous conditions at 4 degrees C. ATRP conditions resulted in controlled polymer growth from rh-GH with low-polydispersity polyPEGMA chains. The rh-GH PEGMA product exhibited properties consistent with the presence of attached hydrophilic polymer chains, namely, high stability to denaturation and proteolysis. The polymerization conditions and conjugation proceeded with retention of the biological activity of the hormone. The rh-GH PEGMA was administered subcutaneously to rats and the activity compared to native rh-GH. The rh-GH PEGMA exhibited similar activity as the native rh-GH in vivo when a daily dose of 40 microg was administered. However, when a higher dose of 120 microg was administered with 3 days between injections the bioavailability of the rh-GH PEGMA was significantly better than that of the native. The results therefore demonstrate that ATRP can be successfully used as a general alternative approach to direct polymer conjugation, namely, PEGylation, to produce PEG-like protein conjugates. This technique can be exploited to design and synthesize protein-polymer derivatives with tailored therapeutic properties.
Collapse
Affiliation(s)
- Johannes Pall Magnusson
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | | | | | | | | |
Collapse
|
31
|
Arad-Haase G, Chuartzman SG, Dagan S, Nevo R, Kouza M, Mai BK, Nguyen HT, Li MS, Reich Z. Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations. Biophys J 2010; 99:238-47. [PMID: 20655852 PMCID: PMC2895382 DOI: 10.1016/j.bpj.2010.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 03/28/2010] [Accepted: 04/01/2010] [Indexed: 11/30/2022] Open
Abstract
Single-molecule manipulation methods provide a powerful means to study protein transitions. Here we combined single-molecule force spectroscopy and steered molecular-dynamics simulations to study the mechanical properties and unfolding behavior of the small enzyme acylphosphatase (AcP). We find that mechanical unfolding of AcP occurs at relatively low forces in an all-or-none fashion and is decelerated in the presence of a ligand, as observed in solution measurements. The prominent energy barrier for the transition is separated from the native state by a distance that is unusually long for alpha/beta proteins. Unfolding is initiated at the C-terminal strand (beta(T)) that lies at one edge of the beta-sheet of AcP, followed by unraveling of the strand located at the other. The central strand of the sheet and the two helices in the protein unfold last. Ligand binding counteracts unfolding by stabilizing contacts between an arginine residue (Arg-23) and the catalytic loop, as well as with beta(T) of AcP, which renders the force-bearing units of the protein resistant to force. This stabilizing effect may also account for the decelerated unfolding of ligand-bound AcP in the absence of force.
Collapse
Affiliation(s)
- Gali Arad-Haase
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Silvia G. Chuartzman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Shlomi Dagan
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Reinat Nevo
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Maksim Kouza
- Department of Physics, Michigan Technological University, Houghton, Michigan
| | - Binh Khanh Mai
- Saigon Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Tien Nguyen
- Saigon Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Ziv Reich
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
32
|
Non-native interactions are critical for mechanical strength in PKD domains. Structure 2010; 17:1582-1590. [PMID: 20004162 PMCID: PMC2862302 DOI: 10.1016/j.str.2009.09.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/23/2009] [Accepted: 09/27/2009] [Indexed: 01/24/2023]
Abstract
Experimental observation has led to the commonly held view that native state protein topology is the principle determinant of mechanical strength. However, the PKD domains of polycystin-1 challenge this assumption: they are stronger than predicted from their native structure. Molecular dynamics simulations suggest that force induces rearrangement to an intermediate structure, with nonnative hydrogen bonds, that resists unfolding. Here we test this hypothesis directly by introducing mutations designed to prevent formation of these nonnative interactions. We find that these mutations, which only moderately destabilize the native state, reduce the mechanical stability dramatically. The results demonstrate that nonnative interactions impart significant mechanical stability, necessary for the mechanosensor function of polycystin-1. Remarkably, such nonnative interactions result from force-induced conformational change: the PKD domain is strengthened by the application of force.
Collapse
|
33
|
Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability. Proc Natl Acad Sci U S A 2010; 107:1989-94. [PMID: 20080695 DOI: 10.1073/pnas.0905796107] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Resolving molecular determinants of mechanical stability of proteins is crucial in the rational design of advanced biomaterials for use in biomedical and nanotechnological applications. Here we present an interdisciplinary study combining bioinformatics screening, steered molecular dynamics simulations, protein engineering, and single-molecule force spectroscopy that explores the mechanical properties of a macro domain protein with mixed alpha + beta topology. The unique architecture is defined by a single seven-stranded beta-sheet in the core of the protein flanked by five alpha-helices. Unlike mechanically stable proteins studied thus far, the macro domain provides the distinct advantage of having the key load-bearing hydrogen bonds (H bonds) buried in the hydrophobic core protected from water attacks. This feature allows direct measurement of the force required to break apart the load-bearing H bonds under locally hydrophobic conditions. Steered molecular dynamics simulations predicted extremely high mechanical stability of the macro domain by using constant velocity and constant force methods. Single-molecule force spectroscopy experiments confirm the exceptional mechanical strength of the macro domain, measuring a rupture force as high as 570 pN. Furthermore, through selective deletion of shielding peptide segments, we examined the same key H bonds under hydrophilic environments in which the beta-strands are exposed to solvent and verify that the high mechanical stability of the macro domain results from excellent shielding of the load-bearing H bonds from competing water. Our study reveals that shielding water accessibility to the load-bearing strands is a critical molecular determinant for enhancing the mechanical stability of proteins.
Collapse
|
34
|
Complementary effects of multi-protein components on biomineralization in vitro. J Struct Biol 2009; 170:83-92. [PMID: 20035875 DOI: 10.1016/j.jsb.2009.12.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Revised: 12/15/2009] [Accepted: 12/17/2009] [Indexed: 01/05/2023]
Abstract
The extracellular matrix (ECM) is composed of mixed protein fibers whose precise composition affects biomineralization. New methods are needed to probe the interactions of these proteins with calcium phosphate mineral and with each other. Here we follow calcium phosphate mineralization on protein fibers self-assembled in vitro from solutions of fibronectin, elastin and their mixture. We probe the surface morphology and mechanical properties of the protein fibers during the early stages. The development of mineral crystals on the protein matrices is also investigated. In physiological mineralization solution, the elastic modulus of the fibers in the fibronectin-elastin mixture increases to a greater extent than that of the fibers from either pure protein. In the presence of fibronectin, longer exposure in the mineral solution leads to the formation of amorphous calcium phosphate particles templated along the self-assembled fibers, while elastin fibers only collect calcium without any mineral observed during early stage. TEM images confirm that small needle-shape crystals are confined inside elastin fibers which suppress the release of mineral outside the fibers during late stage, while hydroxyapatite crystals form when fibronectin is present. These results demonstrate complementary actions of the two ECM proteins fibronectin and elastin to collect cations and template mineral, respectively.
Collapse
|
35
|
Sadler DP, Petrik E, Taniguchi Y, Pullen JR, Kawakami M, Radford SE, Brockwell DJ. Identification of a mechanical rheostat in the hydrophobic core of protein L. J Mol Biol 2009; 393:237-48. [PMID: 19683005 PMCID: PMC2796179 DOI: 10.1016/j.jmb.2009.08.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/23/2009] [Accepted: 08/07/2009] [Indexed: 11/22/2022]
Abstract
The ability of proteins and their complexes to withstand or respond to mechanical stimuli is vital for cells to maintain their structural organisation, to relay external signals and to facilitate unfolding and remodelling. Force spectroscopy using the atomic force microscope allows the behaviour of single protein molecules under an applied extension to be investigated and their mechanical strength to be quantified. protein L, a simple model protein, displays moderate mechanical strength and is thought to unfold by the shearing of two mechanical sub-domains. Here, we investigate the importance of side-chain packing for the mechanical strength of protein L by measuring the mechanical strength of a series of protein L variants containing single conservative hydrophobic volume deletion mutants. Of the five thermodynamically destabilised variants characterised, only one residue (I60V) close to the interface between two mechanical sub-domains was found to differ in mechanical properties to wild type (ΔFI60V–WT = − 36 pN at 447 nm s− 1, ΔxuI60V–WT = 0.2 nm). Φ-value analysis of the unfolding data revealed a highly native transition state. To test whether the number of hydrophobic contacts across the mechanical interface does affect the mechanical strength of protein L, we measured the mechanical properties of two further variants. protein L L10F, which increases core packing but does not enhance interfacial contacts, increased mechanical strength by 13 ± 11 pN at 447 nm s− 1. By contrast, protein L I60F, which increases both core and cross-interface contacts, increased mechanical strength by 72 ± 13 pN at 447 nm s− 1. These data suggest a method by which nature can evolve a varied mechanical response from a limited number of topologies and demonstrate a generic but facile method by which the mechanical strength of proteins can be rationally modified.
Collapse
Affiliation(s)
- David P Sadler
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | | | | | | | |
Collapse
|
36
|
Single-molecule force spectroscopy distinguishes target binding modes of calmodulin. Proc Natl Acad Sci U S A 2009; 106:14361-6. [PMID: 19667195 DOI: 10.1073/pnas.0904654106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The eukaryotic signaling protein calmodulin (CaM) can bind to more than 300 known target proteins to regulate numerous functions in our body in a calcium-dependent manner. How CaM distinguishes between these various targets is still largely unknown. Here, we investigate fluctuations of the complex formation of CaM and its target peptide sequences using single-molecule force spectroscopy by AFM. By applying mechanical force, we can steer a single CaM molecule through its folding energy landscape from the fully unfolded state to the native target-bound state revealing equilibrium fluctuations between numerous intermediate states. We find that the prototypical CaM target sequence skMLCK, a fragment from skeletal muscle myosin light chain kinase, binds to CaM in a highly cooperative way, while only a lower degree of interdomain binding cooperativity emerges for CaMKK, a target peptide from CaM-dependent kinase kinase. We identify minimal binding motifs for both of these peptides, confirming that affinities of target peptides are not exclusively determined by their pattern of hydrophobic anchor residues. Our results reveal an association mode for CaMKK in which the peptide binds strongly to only partially Ca(2+)-saturated CaM. This binding mode might allow for a fine-tuning of the intracellular response to changes in Ca(2+) concentration.
Collapse
|
37
|
Modulating the Mechanical Stability of Extracellular Matrix Protein Tenascin-C in a Controlled and Reversible Fashion. J Mol Biol 2009; 390:820-9. [DOI: 10.1016/j.jmb.2009.05.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 05/14/2009] [Accepted: 05/19/2009] [Indexed: 11/18/2022]
|
38
|
Stacklies W, Vega MC, Wilmanns M, Gräter F. Mechanical network in titin immunoglobulin from force distribution analysis. PLoS Comput Biol 2009; 5:e1000306. [PMID: 19282960 PMCID: PMC2643529 DOI: 10.1371/journal.pcbi.1000306] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 01/27/2009] [Indexed: 11/18/2022] Open
Abstract
The role of mechanical force in cellular processes is increasingly revealed by single molecule experiments and simulations of force-induced transitions in proteins. How the applied force propagates within proteins determines their mechanical behavior yet remains largely unknown. We present a new method based on molecular dynamics simulations to disclose the distribution of strain in protein structures, here for the newly determined high-resolution crystal structure of I27, a titin immunoglobulin (IG) domain. We obtain a sparse, spatially connected, and highly anisotropic mechanical network. This allows us to detect load-bearing motifs composed of interstrand hydrogen bonds and hydrophobic core interactions, including parts distal to the site to which force was applied. The role of the force distribution pattern for mechanical stability is tested by in silico unfolding of I27 mutants. We then compare the observed force pattern to the sparse network of coevolved residues found in this family. We find a remarkable overlap, suggesting the force distribution to reflect constraints for the evolutionary design of mechanical resistance in the IG family. The force distribution analysis provides a molecular interpretation of coevolution and opens the road to the study of the mechanism of signal propagation in proteins in general.
Collapse
Affiliation(s)
- Wolfram Stacklies
- CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai, People's Republic of China
| | - M. Cristina Vega
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC) and Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | | | - Frauke Gräter
- CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai, People's Republic of China
- Bioquant BQ0031, Universität Heidelberg, Heidelberg, Germany
- Max-Planck Institute for Metals Research, Stuttgart, Germany
- * E-mail:
| |
Collapse
|
39
|
Sacquin-Mora S, Lavery R. Modeling the mechanical response of proteins to anisotropic deformation. Chemphyschem 2009; 10:115-8. [PMID: 19006155 DOI: 10.1002/cphc.200800480] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | | |
Collapse
|
40
|
|
41
|
Junker JP, Ziegler F, Rief M. Ligand-dependent equilibrium fluctuations of single calmodulin molecules. Science 2009; 323:633-7. [PMID: 19179531 DOI: 10.1126/science.1166191] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Single-molecule force spectroscopy allows superb mechanical control of protein conformation. We used a custom-built low-drift atomic force microscope to observe mechanically induced conformational equilibrium fluctuations of single molecules of the eukaryotic calcium-dependent signal transducer calmodulin (CaM). From this data, the ligand dependence of the full energy landscape can be reconstructed. We find that calcium ions affect the folding kinetics of the individual CaM domains, whereas target peptides stabilize the already folded structure. Single-molecule data of full length CaM reveal that a wasp venom peptide binds noncooperatively to CaM with 2:1 stoichiometry, whereas a target enzyme peptide binds cooperatively with 1:1 stoichiometry. If mechanical load is applied directly to the target peptide, real-time binding/unbinding transitions can be observed.
Collapse
Affiliation(s)
- Jan Philipp Junker
- Physik Department E22, Technische Universität München, James-Franck-Strasse, 85748 München, Germany
| | | | | |
Collapse
|
42
|
Huang MC, Ye H, Kuan YK, Li MH, Ying JY. Integrated two-step gene synthesis in a microfluidic device. LAB ON A CHIP 2009; 9:276-285. [PMID: 19107285 DOI: 10.1039/b807688j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Herein we present an integrated microfluidic device capable of performing two-step gene synthesis to assemble a pool of oligonucleotides into genes with the desired coding sequence. The device comprised of two polymerase chain reactions (PCRs), temperature-controlled hydrogel valves, electromagnetic micromixer, shuttle micromixer, volume meters, and magnetic beads based solid-phase PCR purification, fabricated using a fast prototyping method without lithography process. The fabricated device is combined with a miniaturized thermal cycler to perform gene synthesis. Oligonucleotides were first assembled into genes by polymerase chain assembly (PCA), and the full-length gene was amplified by a second PCR. The synthesized gene was further separated from the PCR reaction mixture by the solid-phase PCR purification. We have successfully used this device to synthesize a green fluorescent protein fragment (GFPuv) (760 bp), and obtained comparable synthesis yield and error rate with experiments conducted in a PCR tube within a commercial thermal cycler. The resulting error rate determined by DNA sequencing was 1 per 250 bp. To our knowledge, this is the first microfluidic device demonstrating integrated two-step gene synthesis.
Collapse
Affiliation(s)
- Mo Chao Huang
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669
| | | | | | | | | |
Collapse
|
43
|
Fernandes H, Moroni L, van Blitterswijk C, de Boer J. Extracellular matrix and tissue engineering applications. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b822177d] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
44
|
Ng SP, Billings KS, Randles LG, Clarke J. Manipulating the stability of fibronectin type III domains by protein engineering. NANOTECHNOLOGY 2008; 19:384023. [PMID: 21832582 DOI: 10.1088/0957-4484/19/38/384023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have previously shown that a 'weak' fibronectin type III (fnIII) domain can be engineered to have enhanced mechanical strength by replacing the hydrophobic core with the core of a homologous 'strong' fnIII domain. Here we show that engineering the core is a robust method for manipulating the mechanical strength of this class of proteins. We performed an experiment that is the reverse of one described earlier. The hydrophobic core of a 'weak' domain (FNfn10) was grafted into a 'strong' fnIII domain, TNfn3. This newly engineered protein, TNoFNc, is indeed much less mechanically resistant than TNfn3. Interestingly, TNoFNc is very unstable, approximately 10 kcal mol(-1) less stable than FNfn10, yet its mechanical stability is very similar-a clear reflection of the fact that thermodynamic and mechanical stability are unrelated properties, even where they are both assumed to reflect properties of the hydrophobic core.
Collapse
|
45
|
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.
Collapse
|
46
|
Borgia A, Steward A, Clarke J. An Effective Strategy for the Design of Proteins with Enhanced Mechanical Stability. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
47
|
Single molecule force spectroscopy reveals engineered metal chelation is a general approach to enhance mechanical stability of proteins. Proc Natl Acad Sci U S A 2008; 105:11152-7. [PMID: 18685107 DOI: 10.1073/pnas.0803446105] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Significant mechanical stability is an essential feature shared by many elastomeric proteins, which function as molecular springs in a wide variety of biological machinery and biomaterials of superb mechanical properties. Despite the progress in understanding molecular determinants of mechanical stability, it remains challenging to rationally enhance the mechanical stability of proteins. Using single molecule force spectroscopy and protein engineering techniques, we demonstrate that engineered bi-histidine metal chelation can enhance the mechanical stability of proteins significantly and reversibly. Based on simple thermodynamic cycle analysis, we engineered a bi-histidine metal chelation site into various locations of the small protein, GB1, to achieve preferential stabilization of the native state over the mechanical unfolding transition state of GB1 through the binding of metal ions. Our results demonstrate that the metal chelation can enhance the mechanical stability of GB1 by as much as 100 pN. Since bi-histidine metal chelation sites can be easily implemented, engineered metal chelation provides a general methodology to enhance the mechanical stability of a wide variety of proteins. This general approach in protein mechanics will enable the rational tuning of the mechanical stability of proteins. It will not only open new avenues toward engineering proteins of tailored nanomechanical properties, but also provide new approaches to systematically map the mechanical unfolding pathway of proteins.
Collapse
|
48
|
Affiliation(s)
- Alessandro Borgia
- Department of Chemistry, Cambridge University, Medical Research Council Centre for Protein Engineering, Cambridge, CB2 1EW, United Kingdom; ,
| | - Philip M. Williams
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom;
| | - Jane Clarke
- Department of Chemistry, Cambridge University, Medical Research Council Centre for Protein Engineering, Cambridge, CB2 1EW, United Kingdom; ,
| |
Collapse
|
49
|
Probing the mechanical stability of proteins using the atomic force microscope. Biochem Soc Trans 2008; 35:1564-8. [PMID: 18031267 DOI: 10.1042/bst0351564] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mechanical strength of single protein molecules can be investigated by using the atomic force microscope. By applying this technique to a wide range of proteins, it appears that the type of secondary structure and its orientation relative to the extension points are important determinants of mechanical strength. Unlike chemical denaturants, force acts locally and the mechanical strength of a protein may thus appear to be mechanically weak or strong by simply varying the region of the landscape through which the protein is unfolded. Similarly, the effect of ligand binding on the mechanical resistance of a protein may also depend on the relative locations of the binding site and force application. Mechanical deformation may thus facilitate the degradation or remodelling of thermodynamically stable proteins and their complexes in vivo.
Collapse
|
50
|
Borgia A, Steward A, Clarke J. An effective strategy for the design of proteins with enhanced mechanical stability. Angew Chem Int Ed Engl 2008; 47:6900-3. [PMID: 18666188 PMCID: PMC2852638 DOI: 10.1002/anie.200801761] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Indexed: 11/23/2022]
Affiliation(s)
- Alessandro Borgia
- MRC Centre for Protein Engineering, University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge, UK
| | | | | |
Collapse
|