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Mesbah I, Habermann B, Rico F. MechanoProDB: a web-based database for exploring the mechanical properties of proteins. Database (Oxford) 2024; 2024:baae047. [PMID: 38837788 DOI: 10.1093/database/baae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/19/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Abstract
The mechanical stability of proteins is crucial for biological processes. To understand the mechanical functions of proteins, it is important to know the protein structure and mechanical properties. Protein mechanics is usually investigated through force spectroscopy experiments and simulations that probe the forces required to unfold the protein of interest. While there is a wealth of data in the literature on force spectroscopy experiments and steered molecular dynamics simulations of forced protein unfolding, this information is spread and difficult to access by non-experts. Here, we introduce MechanoProDB, a novel web-based database resource for collecting and mining data obtained from experimental and computational works. MechanoProDB provides a curated repository for a wide range of proteins, including muscle proteins, adhesion molecules and membrane proteins. The database incorporates relevant parameters that provide insights into the mechanical stability of proteins and their conformational stability such as the unfolding forces, energy landscape parameters and contour lengths of unfolding steps. Additionally, it provides intuitive annotations of the unfolding pathways of each protein, allowing users to explore the individual steps during mechanical unfolding. The user-friendly interface of MechanoProDB allows researchers to efficiently navigate, search and download data pertaining to specific protein folds or experimental conditions. Users can visualize protein structures using interactive tools integrated within the database, such as Mol*, and plot available data through integrated plotting tools. To ensure data quality and reliability, we have carefully manually verified and curated the data currently available on MechanoProDB. Furthermore, the database also features an interface that enables users to contribute new data and annotations, promoting community-driven comprehensiveness. The freely available MechanoProDB aims to streamline and accelerate research in the field of mechanobiology and biophysics by offering a unique platform for data sharing and analysis. MechanoProDB is freely available at https://mechanoprodb.ibdm.univ-amu.fr.
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Affiliation(s)
- Ismahene Mesbah
- Aix Marseille Univ, INSERM, DyNaMo, Turing Center of Living Systems (CENTURI), Marseille 13009, France
| | - Bianca Habermann
- Aix Marseille Univ, CNRS, IBDM UMR7288, Turing Center of Living Systems (CENTURI), Marseille 13009, France
| | - Felix Rico
- Aix Marseille Univ, INSERM, DyNaMo, Turing Center of Living Systems (CENTURI), Marseille 13009, France
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2
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Valbuena A, Strobl K, Gil-Redondo JC, Valiente L, de Pablo PJ, Mateu MG. Single-Molecule Analysis of Genome Uncoating from Individual Human Rhinovirus Particles, and Modulation by Antiviral Drugs. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304722. [PMID: 37806749 DOI: 10.1002/smll.202304722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/26/2023] [Indexed: 10/10/2023]
Abstract
Infection of humans by many viruses is typically initiated by the internalization of a single virion in each of a few susceptible cells. Thus, the outcome of the infection process may depend on stochastic single-molecule events. A crucial process for viral infection, and thus a target for developing antiviral drugs, is the uncoating of the viral genome. Here a force spectroscopy procedure using an atomic force microscope is implemented to study uncoating for individual human rhinovirus particles. Application of an increasing mechanical force on a virion led to a high force-induced structural transition that facilitated extrusion of the viral RNA molecule without loss of capsid integrity. Application of force to virions that h ad previously extruded the RNA, or to RNA-free capsids, led to a lower force-induced event associated with capsid disruption. The kinetic parameters are determined for each reaction. The high-force event is a stochastic process governed by a moderate free energy barrier (≈20 kcal mol-1 ), which results in a heterogeneous population of structurally weakened virions in which different fractions of the RNA molecule are externalized. The effects of antiviral compounds or capsid mutation on the kinetics of this reaction reveal a correlation between the reaction rate and virus infectivity.
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Affiliation(s)
- Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Klara Strobl
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Carlos Gil-Redondo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, 28049, Madrid, Spain
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3
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Iglesias Rando MR, Gorojovsky N, Zylberman V, Goldbaum FA, Craig PO. Improvement of Cellulomonas fimi endoglucanase CenA by multienzymatic display on a decameric structural scaffold. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12581-6. [PMID: 37212884 DOI: 10.1007/s00253-023-12581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/27/2023] [Accepted: 05/06/2023] [Indexed: 05/23/2023]
Abstract
The development of multifunctional particles using polymeric scaffolds is an emerging technology for many nanobiotechnological applications. Here we present a system for the production of multifunctional complexes, based on the high affinity non-covalent interaction of cohesin and dockerin modules complementary fused to decameric Brucella abortus lumazine synthase (BLS) subunits, and selected target proteins, respectively. The cohesin-BLS scaffold was solubly expressed in high yield in Escherichia coli, and revealed a high thermostability. The production of multienzymatic particles using this system was evaluated using the catalytic domain of Cellulomonas fimi endoglucanase CenA recombinantly fused to a dockerin module. Coupling of the enzyme to the scaffold was highly efficient and occurred with the expected stoichiometry. The decavalent enzymatic complexes obtained showed higher cellulolytic activity and association to the substrate compared to equivalent amounts of the free enzyme. This phenomenon was dependent on the multiplicity and proximity of the enzymes coupled to the scaffold, and was attributed to an avidity effect in the polyvalent enzyme interaction with the substrate. Our results highlight the usefulness of the scaffold presented in this work for the development of multifunctional particles, and the improvement of lignocellulose degradation among other applications. KEY POINTS: • New system for multifunctional particle production using the BLS scaffold • Higher cellulolytic activity of polyvalent endoglucanase compared to the free enzyme • Amount of enzyme associated to cellulose is higher for the polyvalent endoglucanase.
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Affiliation(s)
- Matías R Iglesias Rando
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
| | - Natalia Gorojovsky
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina
| | - Vanesa Zylberman
- Inmunova SA, Gral. San Martín, 25 de Mayo 1021 (CP 1650), Villa Lynch, Buenos Aires, Argentina
| | - Fernando A Goldbaum
- Inmunova SA, Gral. San Martín, 25 de Mayo 1021 (CP 1650), Villa Lynch, Buenos Aires, Argentina
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (CP 1405), Buenos Aires, Argentina
- Centro de Rediseño e Ingeniería de Proteínas (CRIP), UNSAM Campus Miguelete, 25 de Mayo y Francia (CP 1650), Gral. San Martín, Buenos Aires, Argentina
| | - Patricio O Craig
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina.
- CONICET-Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Intendente Güiraldes 2160 (CP 1428), Buenos Aires, Argentina.
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4
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Collagen-like Motifs of SasG: A Novel Fold for Protein Mechanical Strength. J Mol Biol 2023; 435:167980. [PMID: 36708761 DOI: 10.1016/j.jmb.2023.167980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The Staphylococcus aureus surface protein G (SasG) is associated with host colonisation and biofilm formation. As colonisation occurs at the liquid-substrate interface bacteria are subject to a myriad of external forces and, presumably as a consequence, SasG displays extreme mechanical strength. This mechanical phenotype arises from the B-domain; a repetitive region composed of alternating E and G5 subdomains. These subdomains have an unusual structure comprising collagen-like regions capped by triple-stranded β-sheets. To identify the determinants of SasG mechanical strength, we characterised the mechanical phenotype and thermodynamic stability of 18 single substitution variants of a pseudo-wildtype protein. Visualising the mechanically-induced transition state at a residue-level by ϕ-value analysis reveals that the main force-bearing regions are the N- and C-terminal 'Mechanical Clamps' and their side-chain interactions. This is tailored by contacts at the pseudo-hydrophobic core interface. We also describe a novel mechanical motif - the collagen-like region and show that glycine to alanine substitutions, analogous to those found in Osteogenesis Imperfecta (brittle bone disease), result in a significantly reduced mechanical strength.
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5
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Fernández-Ramírez MDC, Ng KKS, Menéndez M, Laurents DV, Hervás R, Carrión-Vázquez M. Expanded Conformations of Monomeric Tau Initiate Its Amyloidogenesis. Angew Chem Int Ed Engl 2022; 62:e202209252. [PMID: 36542681 DOI: 10.1002/anie.202209252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Understanding early amyloidogenesis is key to rationally develop therapeutic strategies. Tau protein forms well-characterized pathological deposits but its aggregation mechanism is still poorly understood. Using single-molecule force spectroscopy based on a mechanical protection strategy, we studied the conformational landscape of the monomeric tau repeat domain (tau-RD244-368 ). We found two sets of conformational states, whose frequency is influenced by mutations and the chemical context. While pathological mutations Δ280K and P301L and a pro-amyloidogenic milieu favored expanded conformations and destabilized local structures, an anti-amyloidogenic environment promoted a compact ensemble, including a conformer whose topology might mask two amyloidogenic segments. Our results reveal that to initiate aggregation, monomeric tau-RD244-368 decreases its polymorphism adopting expanded conformations. This could account for the distinct structures found in vitro and across tauopathies.
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Affiliation(s)
- María Del Carmen Fernández-Ramírez
- Instituto Cajal, IC-CSIC, Avda. Doctor Arce 37, 28002, Madrid, Spain.,Current address: Center for Alzheimer's and Neurodegenerative Diseases, Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kevin Kan-Shing Ng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, 28006, Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias (CIBERES), Spain
| | - Douglas V Laurents
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, 28006, Madrid, Spain
| | - Rubén Hervás
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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6
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Vance TDR, Yip P, Jiménez E, Li S, Gawol D, Byrnes J, Usón I, Ziyyat A, Lee JE. SPACA6 ectodomain structure reveals a conserved superfamily of gamete fusion-associated proteins. Commun Biol 2022; 5:984. [PMID: 36115925 PMCID: PMC9482655 DOI: 10.1038/s42003-022-03883-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
SPACA6 is a sperm-expressed surface protein that is critical for gamete fusion during mammalian sexual reproduction. Despite this fundamental role, little is known about how SPACA6 specifically functions. We elucidated the crystal structure of the SPACA6 ectodomain at 2.2-Å resolution, revealing a two-domain protein containing a four-helix bundle and Ig-like β-sandwich connected via a quasi-flexible linker. This structure is reminiscent of IZUMO1, another gamete fusion-associated protein, making SPACA6 and IZUMO1 founding members of a superfamily of fertilization-associated proteins, herein dubbed the IST superfamily. The IST superfamily is defined structurally by its distorted four-helix bundle and a pair of disulfide-bonded CXXC motifs. A structure-based search of the AlphaFold human proteome identified more protein members to this superfamily; remarkably, many of these proteins are linked to gamete fusion. The SPACA6 structure and its connection to other IST-superfamily members provide a missing link in our knowledge of mammalian gamete fusion.
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Affiliation(s)
- Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Patrick Yip
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Elisabet Jiménez
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028, Barcelona, Spain
| | - Sheng Li
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Diana Gawol
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Isabel Usón
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Ahmed Ziyyat
- Université Paris Cité, CNRS, INSERM, Institut Cochin, F-75014, Paris, France
- Service d'Histologie, d'Embryologie, Biologie de la Reproduction, AP-HP, Hôpital Cochin, F-75014, Paris, France
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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7
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Monroe L, Kihara D. Using steered molecular dynamic tension for assessing quality of computational protein structure models. J Comput Chem 2022; 43:1140-1150. [PMID: 35475517 PMCID: PMC9133218 DOI: 10.1002/jcc.26876] [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: 10/21/2021] [Revised: 02/16/2022] [Accepted: 04/15/2022] [Indexed: 11/12/2022]
Abstract
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their biological function can be properly carried out. Experimentally, the stability of a protein can be measured by several means, among which the pulling experiment using the atomic force microscope (AFM) stands as a unique method. AFM directly measures the resistance from unfolding, which can be quantified from the observed force-extension profile. It has been shown that key features observed in an AFM pulling experiment can be well reproduced by computational molecular dynamics simulations. Here, we applied computational pulling for estimating the accuracy of computational protein structure models under the hypothesis that the structural stability would positively correlated with the accuracy, i.e. the closeness to the native, of a model. We used in total 4929 structure models for 24 target proteins from the Critical Assessment of Techniques of Structure Prediction (CASP) and investigated if the magnitude of the break force, that is, the force required to rearrange the model's structure, from the force profile was sufficient information for selecting near-native models. We found that near-native models can be successfully selected by examining their break forces suggesting that high break force indeed indicates high stability of models. On the other hand, there were also near-native models that had relatively low peak forces. The mechanisms of the stability exhibited by the break forces were explored and discussed.
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Affiliation(s)
- Lyman Monroe
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Purdue University Center for Cancer Research, West Lafayette, IN, 47907, USA
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8
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Liu Z, Moreira RA, Dujmović A, Liu H, Yang B, Poma AB, Nash MA. Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex. NANO LETTERS 2022; 22:179-187. [PMID: 34918516 PMCID: PMC8759085 DOI: 10.1021/acs.nanolett.1c03584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/03/2021] [Indexed: 05/27/2023]
Abstract
We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from its target (CTLA-4), by pulling from eight different anchor residues. We found that pulling on the anticalin from residue 60 or 87 resulted in significantly higher rupture forces and a decrease in koff by 2-3 orders of magnitude over a force range of 50-200 pN. Five of the six internal anchor points gave rise to complexes significantly more stable than N- or C-terminal anchor points, rupturing at up to 250 pN at loading rates of 0.1-10 nN s-1. Anisotropic network modeling and molecular dynamics simulations helped to explain the geometric dependency of mechanostability. These results demonstrate that optimization of attachment residue position on therapeutic binding scaffolds can provide large improvements in binding strength, allowing for mechanical affinity maturation under shear stress without mutation of binding interface residues.
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Affiliation(s)
- Zhaowei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Rodrigo A. Moreira
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - Ana Dujmović
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Byeongseon Yang
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Adolfo B. Poma
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
- International
Center for Research on Innovative Biobased Materials (ICRI-BioM)—International
Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Michael A. Nash
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
- National
Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058 Basel, Switzerland
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9
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Clostridium thermocellum as a Promising Source of Genetic Material for Designer Cellulosomes: An Overview. Catalysts 2021. [DOI: 10.3390/catal11080996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plant biomass-based biofuels have gradually substituted for conventional energy sources thanks to their obvious advantages, such as renewability, huge quantity, wide availability, economic feasibility, and sustainability. However, to make use of the large amount of carbon sources stored in the plant cell wall, robust cellulolytic microorganisms are highly demanded to efficiently disintegrate the recalcitrant intertwined cellulose fibers to release fermentable sugars for microbial conversion. The Gram-positive, thermophilic, cellulolytic bacterium Clostridium thermocellum possesses a cellulolytic multienzyme complex termed the cellulosome, which has been widely considered to be nature’s finest cellulolytic machinery, fascinating scientists as an auspicious source of saccharolytic enzymes for biomass-based biofuel production. Owing to the supra-modular characteristics of the C. thermocellum cellulosome architecture, the cellulosomal components, including cohesin, dockerin, scaffoldin protein, and the plentiful cellulolytic and hemicellulolytic enzymes have been widely used for constructing artificial cellulosomes for basic studies and industrial applications. In addition, as the well-known microbial workhorses are naïve to biomass deconstruction, several research groups have sought to transform them from non-cellulolytic microbes into consolidated bioprocessing-enabling microbes. This review aims to update and discuss the current progress in these mentioned issues, point out their limitations, and suggest some future directions.
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10
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Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
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11
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Vera AM, Galera-Prat A, Wojciechowski M, Różycki B, Laurents DV, Carrión-Vázquez M, Cieplak M, Tinnefeld P. Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization. Structure 2021; 29:587-597.e8. [PMID: 33561387 DOI: 10.1016/j.str.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/25/2020] [Accepted: 01/11/2021] [Indexed: 12/20/2022]
Abstract
Cellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule fluorescence resonance energy transfer and molecular simulations on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.
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Affiliation(s)
- Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Albert Galera-Prat
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland
| | - Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 119, 28006 Madrid, Spain
| | | | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników, 32/46, 02-668 Warsaw, Poland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany
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12
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Hervás R, Del Carmen Fernández-Ramírez M, Galera-Prat A, Suzuki M, Nagai Y, Bruix M, Menéndez M, Laurents DV, Carrión-Vázquez M. Divergent CPEB prion-like domains reveal different assembly mechanisms for a generic amyloid-like fold. BMC Biol 2021; 19:43. [PMID: 33706787 PMCID: PMC7953810 DOI: 10.1186/s12915-021-00967-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/25/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Amyloids are ordered, insoluble protein aggregates, characterized by a cross-β sheet quaternary structure in which molecules in a β-strand conformation are stacked along the filament axis via intermolecular interactions. While amyloids are typically associated with pathological conditions, functional amyloids have also been identified and are present in a wide variety of organisms ranging from bacteria to humans. The cytoplasmic polyadenylation element-binding (CPEB) prion-like protein is an mRNA-binding translation regulator, whose neuronal isoforms undergo activity-dependent aggregation, a process that has emerged as a plausible biochemical substrate for memory maintenance. CPEB aggregation is driven by prion-like domains (PLD) that are divergent in sequence across species, and it remains unknown whether such divergent PLDs follow a similar aggregating assembly pathway. Here, we describe the amyloid-like features of the neuronal Aplysia CPEB (ApCPEB) PLD and compare them to those of the Drosophila ortholog, Orb2 PLD. RESULTS Using in vitro single-molecule and bulk biophysical methods, we find transient oligomers and mature amyloid-like filaments that suggest similarities in the late stages of the assembly pathway for both ApCPEB and Orb2 PLDs. However, while prior to aggregation the Orb2 PLD monomer remains mainly as a random coil in solution, ApCPEB PLD adopts a diversity of conformations comprising α-helical structures that evolve to coiled-coil species, indicating structural differences at the beginning of their amyloid assembly pathways. CONCLUSION Our results indicate that divergent PLDs of CPEB proteins from different species retain the ability to form a generic amyloid-like fold through different assembly mechanisms.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC, Avda. Doctor Arce 37, E-28002, Madrid, Spain. .,Present address: School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | | | | | - Mari Suzuki
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Present address: Diabetic Neuropathy Project, Department of Sensory and Motor Systems, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Present address: Department of Neurology, Faculty of Medicine, Kindai University, Osaka-Sayama, Osaka, Japan
| | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias (CIBERES), C/ Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain
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13
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Vance TDR, Ye Q, Conroy B, Davies PL. Essential role of calcium in extending RTX adhesins to their target. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100036. [PMID: 32984811 PMCID: PMC7493085 DOI: 10.1016/j.yjsbx.2020.100036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/12/2020] [Accepted: 09/02/2020] [Indexed: 11/25/2022]
Abstract
Elongated beta-sandwich repeats are a major part of bacterial RTX adhesins. The repeats are arranged in tandem to extend away from the bacterial surface. Calcium ions are coordinated in the linkers between repeats to stiffen the protein. Rigidification of the tandem repeats further helps extension of the adhesin. The repeats differ greatly between species, but all have Ca2+ in their linkers.
RTX adhesins are long, multi-domain proteins present on the outer membrane of many Gram-negative bacteria. From this vantage point, adhesins use their distal ligand-binding domains for surface attachment leading to biofilm formation. To expand the reach of the ligand-binding domains, RTX adhesins maintain a central extender region of multiple tandem repeats, which makes up most of the proteins’ large molecular weight. Alignments of the 10-15-kDa extender domains show low sequence identity between adhesins. Here we have produced and structurally characterized protein constructs of four tandem repeats (tetra-tandemers) from two different RTX adhesins. In comparing the tetra-tandemers to each other and already solved structures from Marinomonas primoryensis and Salmonella enterica, the extender domains fold as diverse beta-sandwich structures with widely differing calcium contents. However, all the tetra-tandemers have at least one calcium ion coordinated in the linker region between beta-sandwich domains whose role appears to be the rigidification of the extender region to help the adhesin extend its reach.
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Affiliation(s)
- Tyler D R Vance
- Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada
| | - Qilu Ye
- Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada
| | - Brigid Conroy
- Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Science, Queen's University Kingston ON, Canada
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14
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Moreira RA, Chwastyk M, Baker JL, Guzman HV, Poma AB. Quantitative determination of mechanical stability in the novel coronavirus spike protein. NANOSCALE 2020; 12:16409-16413. [PMID: 32725017 DOI: 10.1039/d0nr03969a] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report on the novel observation about the gain in nanomechanical stability of the SARS-CoV-2 (CoV2) spike (S) protein in comparison with SARS-CoV from 2002 (CoV1). Our findings have several biological implications in the subfamily of coronaviruses, as they suggest that the receptor binding domain (RBD) (∼200 amino acids) plays a fundamental role as a damping element of the massive viral particle's motion prior to cell-recognition, while also facilitating viral attachment, fusion and entry. The mechanical stability via pulling of the RBD is 250 pN and 200 pN for CoV2 and CoV1 respectively, and the additional stability observed for CoV2 (∼50 pN) might play a role in the increasing spread of COVID-19.
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Affiliation(s)
- Rodrigo A Moreira
- Biosystems and Soft Matter divison, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland.
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15
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Galera-Prat A, Vera AM, Moraïs S, Vazana Y, Bayer EA, Carrión-Vázquez M. Impact of scaffoldin mechanostability on cellulosomal activity. Biomater Sci 2020; 8:3601-3610. [PMID: 32232253 DOI: 10.1039/c9bm02052g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lignocellulose is the most abundant renewable carbon source in the biosphere. However, the main bottleneck in its conversion to produce second generation biofuels is the saccharification step: the hydrolysis of lignocellulosic material into soluble fermentable sugars. Some anaerobic bacteria have developed an extracellular multi-enzyme complex called the cellulosome that efficiently degrades cellulosic substrates. Cellulosome complexes rely on enzyme-integrating scaffoldins that are large non-catalytic scaffolding proteins comprising several cohesin modules and additional functional modules that mediate the anchoring of the complex to the cell surface and the specific binding to its cellulosic substrate. It was proposed that mechanical forces may affect the cohesins positioned between the cell- and cellulose-anchoring points in the so-called connecting region. Consequently, the mechanical resistance of cohesins within the scaffoldin is of great importance, both to understand cellulosome function and as a parameter of industrial interest, to better mimic natural complexes through the use of the established designer cellulosome technology. Here we study how the mechanical stability of cohesins in a scaffoldin affects the enzymatic activity of a cellulosome. We found that when a cohesin of low mechanical stability is positioned in the connecting region of a scaffoldin, the activity of the resulting cellulosome is reduced as opposed to a cohesin of higher mechanical stability. This observation directly relates mechanical stability of the scaffoldin-borne cohesins to cellulosome activity and provides a rationale for the design of artificial cellulosomes for industrial applications, by incorporating mechanical stability as a new industrial parameter in the biotechnology toolbox.
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Affiliation(s)
- Albert Galera-Prat
- Instituto Cajal, Department of Molecular, Cellular and Developmental Neurobiology. IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain.
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16
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Mioduszewski Ł, Różycki B, Cieplak M. Pseudo-Improper-Dihedral Model for Intrinsically Disordered Proteins. J Chem Theory Comput 2020; 16:4726-4733. [PMID: 32436706 PMCID: PMC7588027 DOI: 10.1021/acs.jctc.0c00338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a new coarse-grained Cα-based protein model with a nonradial multibody pseudo-improper-dihedral potential that is transferable, time-independent, and suitable for molecular dynamics. It captures the nature of backbone and side-chain interactions between amino acid residues by adapting a simple improper dihedral term for a one-bead-per-residue model. It is parameterized for intrinsically disordered proteins and applicable to simulations of such proteins and their assemblies on millisecond time scales.
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Affiliation(s)
- Łukasz Mioduszewski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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17
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Transient knots in intrinsically disordered proteins and neurodegeneration. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:79-103. [PMID: 32828471 DOI: 10.1016/bs.pmbts.2020.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We provide a brief overview of the topological features found in structured proteins and of the dynamical processes that involve knots. We then discuss the knotted states that arise in the intrinsically disordered polyglutamine and α-synuclein. We argue that the existence of the knotted conformations stalls degradation by proteases and thus enhances aggregation. This mechanism works if the length of a peptide chain exceeds a threshold, as in the Huntington disease. We also study the cavities that form within the conformations of the disordered proteins. The volume of the cavities varies in time in a way that is different than that of the radius of gyration or the end-to-end distance. In addition, we study the traffic between the conformational basins and identify patterns associated with the deep and shallow knots. The results are obtained by molecular dynamics simulations that use coarse-grained and all-atom models (with and without the explicit solvent).
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18
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Mora M, Stannard A, Garcia-Manyes S. The nanomechanics of individual proteins. Chem Soc Rev 2020; 49:6816-6832. [DOI: 10.1039/d0cs00426j] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This tutorial review provides an overview of the single protein force spectroscopy field, including the main techniques and the basic tools for analysing the data obtained from the single molecule experiments.
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Affiliation(s)
- Marc Mora
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Andrew Stannard
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
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19
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Yuan G, Liu H, Ma Q, Li X, Nie J, Zuo J, Zheng P. Single-Molecule Force Spectroscopy Reveals that Iron-Ligand Bonds Modulate Proteins in Different Modes. J Phys Chem Lett 2019; 10:5428-5433. [PMID: 31433648 DOI: 10.1021/acs.jpclett.9b01573] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The iron-amino acid interactions Fe-O(Glu/Asp), Fe-N(His), and Fe-S(Cys) are the three major iron-ligand bonds in proteins. To compare their properties in proteins, we used atomic force microscopy (AFM)-based single-molecule force spectroscopy to investigate a superoxide reductase (Fe(III)-SOR) with all three types of bonds forming an Fe(His)4CysGlu center. We first found that Apo-SOR without bound iron showed multiple unfolding pathways only from the β-barrel core. Then, using Holo-SOR with a ferric ion, we found that a single Fe-O(Glu) bond can tightly connect the flexible N-terminal fragment to the β-barrel and stabilize the whole protein, showing a complete protein unfolding scenario, while the single Fe-N(His) bond was weak and unable to provide such a stabilization. Moreover, when multiple Fe-N bonds are present, a similar stabilization effect can be achieved. Our results showed that the iron-ligand bond modulates protein structure and stability in different modes at the single-bond level.
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Affiliation(s)
- Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Huaxing Liu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Qun Ma
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Jinglin Zuo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , People's Republic of China
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20
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Wang Y, Leng L, Islam MK, Liu F, Lin CSK, Leu SY. Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization. Int J Mol Sci 2019; 20:ijms20133354. [PMID: 31288425 PMCID: PMC6651384 DOI: 10.3390/ijms20133354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence in the utilization of cellulosic biomass. Significant progress has been achieved in revealing the structures and functions of cellulosomes, but a knowledge gap still exists in understanding the interaction between cellulosome and lignocellulosic substrate for those derived from biorefinery pretreatment of agricultural crops. The cellulosomic saccharification of lignocellulose is affected by various substrate-related physical and chemical factors, including native (untreated) wood lignin content, the extent of lignin and xylan removal by pretreatment, lignin structure, substrate size, and of course substrate pore surface area or substrate accessibility to cellulose. Herein, we summarize the cellulosome structure, substrate-related factors, and regulatory mechanisms in the host cells. We discuss the latest advances in specific strategies of cellulosome-induced hydrolysis, which can function in the reaction kinetics and the overall progress of biorefineries based on lignocellulosic feedstocks.
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Affiliation(s)
- Ying Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Ling Leng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Md Khairul Islam
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Fanghua Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
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21
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Barruetabeña N, Alonso-Lerma B, Galera-Prat A, Joudeh N, Barandiaran L, Aldazabal L, Arbulu M, Alcalde M, De Sancho D, Gavira JA, Carrion-Vazquez M, Perez-Jimenez R. Resurrection of efficient Precambrian endoglucanases for lignocellulosic biomass hydrolysis. Commun Chem 2019. [DOI: 10.1038/s42004-019-0176-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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22
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Gunnoo M, Cazade PA, Orlowski A, Chwastyk M, Liu H, Ta DT, Cieplak M, Nash M, Thompson D. Steered molecular dynamics simulations reveal the role of Ca 2+ in regulating mechanostability of cellulose-binding proteins. Phys Chem Chem Phys 2019; 20:22674-22680. [PMID: 30132772 DOI: 10.1039/c8cp00925b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The conversion of cellulosic biomass into biofuels requires degradation of the biomass into fermentable sugars. The most efficient natural cellulase system for carrying out this conversion is an extracellular multi-enzymatic complex named the cellulosome. In addition to temperature and pH stability, mechanical stability is important for functioning of cellulosome domains, and experimental techniques such as Single Molecule Force Spectroscopy (SMFS) have been used to measure the mechanical strength of several cellulosomal proteins. Molecular dynamics computer simulations provide complementary atomic-resolution quantitative maps of domain mechanical stability for identification of experimental leads for protein stabilization. In this study, we used multi-scale steered molecular dynamics computer simulations, benchmarked against new SMFS measurements, to measure the intermolecular contacts that confer high mechanical stability to a family 3 Carbohydrate Binding Module protein (CBM3) derived from the archetypal Clostridium thermocellum cellulosome. Our data predicts that electrostatic interactions in the calcium binding pocket modulate the mechanostability of the cellulose-binding module, which provides an additional design rule for the rational re-engineering of designer cellulosomes for biotechnology. Our data offers new molecular insights into the origins of mechanostability in cellulose binding domains and gives leads for synthesis of more robust cellulose-binding protein modules. On the other hand, simulations predict that insertion of a flexible strand can promote alternative unfolding pathways and dramatically reduce the mechanostability of the carbohydrate binding module, which gives routes to rational design of tailormade fingerprint complexes for force spectroscopy experiments.
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Affiliation(s)
- Melissabye Gunnoo
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX, Ireland.
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23
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Deng Y, Wu T, Wang M, Shi S, Yuan G, Li X, Chong H, Wu B, Zheng P. Enzymatic biosynthesis and immobilization of polyprotein verified at the single-molecule level. Nat Commun 2019; 10:2775. [PMID: 31235796 PMCID: PMC6591319 DOI: 10.1038/s41467-019-10696-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/23/2019] [Indexed: 11/09/2022] Open
Abstract
The recent development of chemical and bio-conjugation techniques allows for the engineering of various protein polymers. However, most of the polymerization process is difficult to control. To meet this challenge, we develop an enzymatic procedure to build polyprotein using the combination of a strict protein ligase OaAEP1 (Oldenlandia affinis asparaginyl endopeptidases 1) and a protease TEV (tobacco etch virus). We firstly demonstrate the use of OaAEP1-alone to build a sequence-uncontrolled ubiquitin polyprotein and covalently immobilize the coupled protein on the surface. Then, we construct a poly-metalloprotein, rubredoxin, from the purified monomer. Lastly, we show the feasibility of synthesizing protein polymers with rationally-controlled sequences by the synergy of the ligase and protease, which are verified by protein unfolding using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Thus, this study provides a strategy for polyprotein engineering and immobilization.
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Affiliation(s)
- Yibing Deng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Mengdi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Guodong Yuan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Xi Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Hanchung Chong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China.
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24
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Poma AB, Li MS, Theodorakis PE. Generalization of the elastic network model for the study of large conformational changes in biomolecules. Phys Chem Chem Phys 2019; 20:17020-17028. [PMID: 29904772 DOI: 10.1039/c8cp03086c] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching of proteins, folding and thermal unfolding). Here, we extend the capabilities of the EN model by using a harmonic approximation described by Lennard-Jones (LJ) interactions for far contacts and native contacts obtained from the standard overlap criterion as in the case of Gō-like models. While our model is validated against the EN model by reproducing the equilibrium properties for a number of proteins, we also show that the model is suitable for the study of large conformation changes by providing various examples. In particular, this is illustrated on the basis of pulling simulations that predict with high accuracy the experimental data on the rupture force of the studied proteins. Furthermore, in the case of DDFLN4 protein, our pulling simulations highlight the advantages of our model with respect to Gō-like approaches, where the latter fail to reproduce previous results obtained by all-atom simulations that predict an additional characteristic peak for this protein. In addition, folding simulations of small peptides yield different folding times for α-helix and β-hairpin, in agreement with experiment, in this way providing further opportunities for the application of our model in studying large conformational changes of proteins. In contrast to the EN model, our model is suitable for both normal mode analysis and molecular dynamics simulation. We anticipate that the proposed model will find applications in a broad range of problems in biology, including, among others, protein folding and thermal unfolding.
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Affiliation(s)
- Adolfo B Poma
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
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25
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Milles LF, Unterauer EM, Nicolaus T, Gaub HE. Calcium stabilizes the strongest protein fold. Nat Commun 2018; 9:4764. [PMID: 30420680 PMCID: PMC6232131 DOI: 10.1038/s41467-018-07145-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022] Open
Abstract
Staphylococcal pathogens adhere to their human targets with exceptional resilience to mechanical stress, some propagating force to the bacterium via small, Ig-like folds called B domains. We examine the mechanical stability of these folds using atomic force microscopy-based single-molecule force spectroscopy. The force required to unfold a single B domain is larger than 2 nN – the highest mechanostability of a protein to date by a large margin. B domains coordinate three calcium ions, which we identify as crucial for their extreme mechanical strength. When calcium is removed through chelation, unfolding forces drop by a factor of four. Through systematic mutations in the calcium coordination sites we can tune the unfolding forces from over 2 nN to 0.15 nN, and dissect the contribution of each ion to B domain mechanostability. Their extraordinary strength, rapid refolding and calcium-tunable force response make B domains interesting protein design targets. Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.
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Affiliation(s)
- Lukas F Milles
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany.
| | - Eduard M Unterauer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany
| | - Thomas Nicolaus
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, Amalienstr. 54, 80799, Munich, Germany.
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26
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Fernández-Ramírez MDC, Hervás R, Galera-Prat A, Laurents DV, Carrión-Vázquez M. Efficient and simplified nanomechanical analysis of intrinsically disordered proteins. NANOSCALE 2018; 10:16857-16867. [PMID: 30168565 DOI: 10.1039/c8nr02785d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) lack a tertiary structure. Amyloidogenic IDPs (aIDPs) in particular have attracted great interest due to their implication in several devastating diseases as well as in critical biological functions. However, the conformational changes that trigger amyloid formation in aIDPs are largely unknown. aIDPs' conformational polymorphism at the monomer level encumbers their study using bulk techniques. Single-molecule techniques like atomic force microscopy-based single-molecule force spectroscopy represent a promising approach and a "carrier-guest" strategy, in which the protein of interest is mechanically protected, was developed to overcome the spurious signals from the noisy proximal region. However, since the carrier and single-molecule markers have similar mechanostabilities, their signals can intermingle in the force-extension recordings, making peak selection and analysis very laborious, cumbersome and prone to error for the non-expert. Here we have developed a new carrier, the c8C module from the CipC scaffoldin, with a higher mechanostability so that the signals from the protected protein will appear at the end of the recordings. This assures an accurate, more efficient and expert-independent analysis, simplifying both the selection and analysis of the single-molecule data. Furthermore, this modular design can be integrated into any SMFS polyprotein-based vector, thus constituting a useful utensil in the growing toolbox of protein nanomechanics.
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Song W, Zhao Y, Wu Y, Li Z, Lv H, Li S, Jiang Y, Song C, Wang F, Huang Y. Fabrication, characterization and biocompatibility of collagen/oxidized regenerated cellulose-Ca composite scaffold for carrying Schwann cells. Int J Biol Macromol 2018; 119:1195-1203. [PMID: 30110602 DOI: 10.1016/j.ijbiomac.2018.08.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 01/14/2023]
Abstract
Schwann cell (SC) is the primary structural and functional part of the peripheral nervous system, and it plays a key role in the repair and regeneration of peripheral nerve. In order to develop a suitable scaffold for SC nerve tissue engineering, three kinds of scaffolds, including pristine collagen, pure oxidized regenerated cellulose-Ca (ORCCa) and collagen/ORC-Ca composite scaffolds, have been fabricated for carrying SC in this study. SC is then seeded on the scaffolds to form SC-scaffold nerve tissue engineering composites and evaluate their biocompatibility. The chemical and physical structure of the scaffolds are investigated by FTIR, NMR and SEM. The wettability of the collagen/ORC-Ca composite scaffold is close to that of pristine collagen, and the tensile strength of the composite scaffold (0.58 MPa) is better than that of pristine collagen (0.36 MPa). Cytotoxicity, cell proliferation, cell adhesion and western blotting assays are conducted to evaluate the biocompatibility and properties of different scaffolds. The results show that the three scaffolds exhibit no toxicity, and the proliferation rate of SC on the collagen/ORC-Ca composite scaffold is significantly higher than that of the other scaffolds (p < 0.05). The number of the adhesion cells on the composite scaffold (244.67 ± 13.02) is much more than that in the pure ORC-Ca group (p < 0.01). Furthermore, the expression of N-Cadheri and PMP22 proteins in the collagen/ORC-Ca composite scaffold is significantly superior to the other two scaffolds (both p < 0.01). Therefore, it could be concluded that the collagen/ORC-Ca composite is a promising candidate as a scaffold for carrying SC to form nerve tissue engineering composites in order to assist the peripheral nervous in the repair and regeneration.
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Affiliation(s)
- Wenli Song
- Harbin Sport University, Harbin 150008, China
| | - Yuhua Zhao
- Harbin Sport University, Harbin 150008, China
| | - Yadong Wu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China.
| | - Zhipeng Li
- Harbin Sport University, Harbin 150008, China
| | - Hui Lv
- The First Affiliated Hospital of Harbin Medical University, Harbin 150007, China
| | - Siyu Li
- Harbin Medical University (Da Qing), Da Qing 163319, China
| | - Yue Jiang
- Harbin Medical University (Da Qing), Da Qing 163319, China
| | - Chun Song
- The First Affiliated Hospital of Harbin Medical University, Harbin 150007, China
| | - Fang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Yudong Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, China
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Mechanical architecture and folding of E. coli type 1 pilus domains. Nat Commun 2018; 9:2758. [PMID: 30013059 PMCID: PMC6048123 DOI: 10.1038/s41467-018-05107-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 05/03/2018] [Indexed: 12/16/2022] Open
Abstract
Uropathogenic Escherichia coli attach to tissues using pili type 1. Each pilus is composed by thousands of coiled FimA domains followed by the domains of the tip fibrillum, FimF-FimG-FimH. The domains are linked by non-covalent β-strands that must resist mechanical forces during attachment. Here, we use single-molecule force spectroscopy to measure the mechanical contribution of each domain to the stability of the pilus and monitor the oxidative folding mechanism of a single Fim domain assisted by periplasmic FimC and the oxidoreductase DsbA. We demonstrate that pilus domains bear high mechanical stability following a hierarchy by which domains close to the tip are weaker than those close to or at the pilus rod. During folding, this remarkable stability is achieved by the intervention of DsbA that not only forms strategic disulfide bonds but also serves as a chaperone assisting the folding of the domains. The pilus type 1 of uropathogenic E. coli must resist mechanical forces to remain attached to the epithelium. Here the authors use single-molecule force spectroscopy to demonstrate a hierarchy of mechanical stability among the pilus domains and show that the oxidoreductase DsbA also acts as a folding chaperone on the domains.
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Verdorfer T, Gaub HE. Ligand Binding Stabilizes Cellulosomal Cohesins as Revealed by AFM-based Single-Molecule Force Spectroscopy. Sci Rep 2018; 8:9634. [PMID: 29941985 PMCID: PMC6018229 DOI: 10.1038/s41598-018-27085-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022] Open
Abstract
The cohesin-dockerin receptor-ligand family is the key element in the formation of multi-enzyme lignocellulose-digesting extracellular complexes called cellulosomes. Changes in a receptor protein upon binding of a ligand - commonly referred to as allostery - are not just essential for signalling, but may also alter the overall mechanical stability of a protein receptor. Here, we measured the change in mechanical stability of a library of cohesin receptor domains upon binding of their dockerin ligands in a multiplexed atomic force microscopy-based single-molecule force spectroscopy experiment. A parallelized, cell-free protein expression and immobilization protocol enables rapid mechanical phenotyping of an entire library of constructs with a single cantilever and thus ensures high throughput and precision. Our results show that dockerin binding increases the mechanical stability of every probed cohesin independently of its original folding strength. Furthermore, our results indicate that certain cohesins undergo a transition from a multitude of different folds or unfolding pathways to a single stable fold upon binding their ligand.
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Affiliation(s)
- Tobias Verdorfer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799, Munich, Germany.
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799, Munich, Germany
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Nadler H, Shaulov L, Blitsman Y, Mordechai M, Jopp J, Sal-Man N, Berkovich R. Deciphering the Mechanical Properties of Type III Secretion System EspA Protein by Single Molecule Force Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6261-6270. [PMID: 29726683 DOI: 10.1021/acs.langmuir.8b01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial pathogens inject virulence factors into host cells during bacterial infections using type III secretion systems. In enteropathogenic Escherichia coli, this system contains an external filament, formed by a self-oligomerizing protein called E. coli secreted protein A (EspA). The EspA filament penetrates the thick viscous mucus layer to facilitate the attachment of the bacteria to the gut-epithelium. To do that, the EspA filament requires noteworthy mechanical endurance considering the mechanical shear stresses found within the intestinal tract. To date, the mechanical properties of the EspA filament and the structural and biophysical knowledge of monomeric EspA are very limited, mostly due to the strong tendency of the protein to self-oligomerize. To overcome this limitation, we employed a single molecule force spectroscopy (SMFS) technique and studied the mechanical properties of EspA. Force extension dynamic of (I91)4-EspA-(I91)4 chimera revealed two structural unfolding events occurring at low forces during EspA unfolding, thus indicating no unique mechanical stability of the monomeric protein. SMFS examination of purified monomeric EspA protein, treated by a gradually refolding protocol, exhibited similar mechanical properties as the EspA protein within the (I91)4-EspA-(I91)4 chimera. Overall, our results suggest that the mechanical integrity of the EspA filament likely originates from the interactions between EspA monomers and not from the strength of an individual monomer.
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Affiliation(s)
- Hila Nadler
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Lihi Shaulov
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Yossi Blitsman
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Moran Mordechai
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Jürgen Jopp
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Neta Sal-Man
- Department of Microbiology, Immunology and Genetics , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
| | - Ronen Berkovich
- Department of Chemical Engineering , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
- The Ilse Katz Institute for Nanoscale Science and Technology , Ben-Gurion University of the Negev , Beer Sheva 8410501 , Israel
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Galera-Prat A, Moraïs S, Vazana Y, Bayer EA, Carrión-Vázquez M. The cohesin module is a major determinant of cellulosome mechanical stability. J Biol Chem 2018; 293:7139-7147. [PMID: 29567834 PMCID: PMC5950008 DOI: 10.1074/jbc.ra117.000644] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Indexed: 01/20/2023] Open
Abstract
Cellulosomes are bacterial protein complexes that bind and efficiently degrade lignocellulosic substrates. These are formed by multimodular scaffolding proteins known as scaffoldins, which comprise cohesin modules capable of binding dockerin-bearing enzymes and usually a carbohydrate-binding module that anchors the system to a substrate. It has been suggested that cellulosomes bound to the bacterial cell surface might be exposed to significant mechanical forces. Accordingly, the mechanical properties of these anchored cellulosomes may be important to understand and improve cellulosome function. Here we used single-molecule force spectroscopy to study the mechanical properties of selected cohesin modules from scaffoldins of different cellulosomes. We found that cohesins located in the region connecting the cell and the substrate are more robust than those located outside these two anchoring points. This observation applies to cohesins from primary scaffoldins (i.e. those that directly bind dockerin-bearing enzymes) from different cellulosomes despite their sequence differences. Furthermore, we also found that cohesin nanomechanics (specifically, mechanostability and the position of the mechanical clamp of cohesin) are not significantly affected by other cellulosomal components, including linkers between cohesins, multiple cohesin repeats, and dockerin binding. Finally, we also found that cohesins (from both the connecting and external regions) have poor refolding efficiency but similar refolding rates, suggesting that the high mechanostability of connecting cohesins may be an evolutionarily conserved trait selected to minimize the occurrence of cohesin unfolding, which could irreversibly damage the cellulosome. We conclude that cohesin mechanostability is a major determinant of the overall mechanical stability of the cellulosome.
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Affiliation(s)
- Albert Galera-Prat
- Instituto Cajal, IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain
| | - Sarah Moraïs
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yael Vazana
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-CSIC, Avenida Doctor Arce 37, 28002 Madrid, Spain; Instituto Madrileño de Estudios Avanzados en Nanociencia, Cantoblanco, 28049 Madrid, Spain.
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Galera-Prat A, Pantoja-Uceda D, Laurents DV, Carrión-Vázquez M. Solution conformation of a cohesin module and its scaffoldin linker from a prototypical cellulosome. Arch Biochem Biophys 2018; 644:1-7. [PMID: 29486159 DOI: 10.1016/j.abb.2018.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Accepted: 02/23/2018] [Indexed: 11/26/2022]
Abstract
Bacterial cellulases are drawing increased attention as a means to obtain plentiful chemical feedstocks and fuels from renewable lignocellulosic biomass sources. Certain bacteria deploy a large extracellular multi-protein complex, called the cellulosome, to degrade cellulose. Scaffoldin, a key non-catalytic cellulosome component, is a large protein containing a cellulose-specific carbohydrate-binding module and several cohesin modules which bind and organize the hydrolytic enzymes. Despite the importance of the structure and protein/protein interactions of the cohesin module in the cellulosome, its structure in solution has remained unknown to date. Here, we report the backbone 1H, 13C and 15N NMR assignments of the Cohesin module 5 from the highly stable and active cellulosome from Clostridium thermocellum. These data reveal that this module adopts a tightly packed, well folded and rigid structure in solution. Furthermore, since in scaffoldin, the cohesin modules are connected by linkers we have also characterized the conformation of a representative linker segment using NMR spectroscopy. Analysis of its chemical shift values revealed that this linker is rather stiff and tends to adopt extended conformations. This suggests that the scaffoldin linkers act to minimize interactions between cohesin modules. These results pave the way towards solution studies on cohesin/dockerin's fascinating dual-binding mode.
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Affiliation(s)
| | - David Pantoja-Uceda
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 199, E-28006, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 199, E-28006, Madrid, Spain.
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Wojciechowski M, Różycki B, Huy PDQ, Li MS, Bayer EA, Cieplak M. Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module. Sci Rep 2018; 8:5051. [PMID: 29568013 PMCID: PMC5864761 DOI: 10.1038/s41598-018-23380-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/05/2018] [Indexed: 01/09/2023] Open
Abstract
The assembly of the polysaccharide degradating cellulosome machinery is mediated by tight binding between cohesin and dockerin domains. We have used an empirical model known as FoldX as well as molecular mechanics methods to determine the free energy of binding between a cohesin and a dockerin from Clostridium thermocellum in two possible modes that differ by an approximately 180° rotation. Our studies suggest that the full-length wild-type complex exhibits dual binding at room temperature, i.e., the two modes of binding have comparable probabilities at equilibrium. The ability to bind in the two modes persists at elevated temperatures. However, single-point mutations or truncations of terminal segments in the dockerin result in shifting the equilibrium towards one of the binding modes. Our molecular dynamics simulations of mechanical stretching of the full-length wild-type cohesin-dockerin complex indicate that each mode of binding leads to two kinds of stretching pathways, which may be mistakenly taken as evidence of dual binding.
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Affiliation(s)
- Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Bartosz Różycki
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Pham Dinh Quoc Huy
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
- Institute for Computational Sciences and Technology, SBI building, Quang Trung Software city, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668, Warsaw, Poland.
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Gunnoo M, Cazade PA, Bayer EA, Thompson D. Molecular simulations reveal that a short helical loop regulates thermal stability of type I cohesin–dockerin complexes. Phys Chem Chem Phys 2018; 20:28445-28451. [DOI: 10.1039/c8cp04800b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Re-engineering linker regions to boost the thermal stability of protein–protein complexes.
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Affiliation(s)
- Melissabye Gunnoo
- Department of Physics
- Bernal Institute, University of Limerick
- V94 T9PX
- Ireland
| | - Pierre-André Cazade
- Department of Physics
- Bernal Institute, University of Limerick
- V94 T9PX
- Ireland
| | - Edward A. Bayer
- Department of Biomolecular Sciences, Faculty of Biochemistry, Weizmann Institute of Science
- Rehovot
- Israel
| | - Damien Thompson
- Department of Physics
- Bernal Institute, University of Limerick
- V94 T9PX
- Ireland
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35
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Verdorfer T, Bernardi RC, Meinhold A, Ott W, Luthey-Schulten Z, Nash MA, Gaub HE. Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics. J Am Chem Soc 2017; 139:17841-17852. [PMID: 29058444 PMCID: PMC5737924 DOI: 10.1021/jacs.7b07574] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cellulosomes are polyprotein machineries that efficiently degrade cellulosic material. Crucial to their function are scaffolds consisting of highly homologous cohesin domains, which serve a dual role by coordinating a multiplicity of enzymes as well as anchoring the microbe to its substrate. Here we combined two approaches to elucidate the mechanical properties of the main scaffold ScaA of Acetivibrio cellulolyticus. A newly developed parallelized one-pot in vitro transcription-translation and protein pull-down protocol enabled high-throughput atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) measurements of all cohesins from ScaA with a single cantilever, thus promising improved relative force comparability. Albeit very similar in sequence, the hanging cohesins showed considerably lower unfolding forces than the bridging cohesins, which are subjected to force when the microbe is anchored to its substrate. Additionally, all-atom steered molecular dynamics (SMD) simulations on homology models offered insight into the process of cohesin unfolding under force. Based on the differences among the individual force propagation pathways and their associated correlation communities, we designed mutants to tune the mechanical stability of the weakest hanging cohesin. The proposed mutants were tested in a second high-throughput AFM SMFS experiment revealing that in one case a single alanine to glycine point mutation suffices to more than double the mechanical stability. In summary, we have successfully characterized the force induced unfolding behavior of all cohesins from the scaffoldin ScaA, as well as revealed how small changes in sequence can have large effects on force resilience in cohesin domains. Our strategy provides an efficient way to test and improve the mechanical integrity of protein domains in general.
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Affiliation(s)
- Tobias Verdorfer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Rafael C Bernardi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aylin Meinhold
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Wolfgang Ott
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Zaida Luthey-Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael A Nash
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), 4058 Basel, Switzerland
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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36
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37
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Chwastyk M, Vera AM, Galera-Prat A, Gunnoo M, Thompson D, Carrión-Vázquez M, Cieplak M. Non-local effects of point mutations on the stability of a protein module. J Chem Phys 2017; 147:105101. [DOI: 10.1063/1.4999703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668 Warsaw, Poland
| | - Andrés M. Vera
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, (CSIC), Ave. Doctor Arce, 37, 28002 Madrid, Spain
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, (CSIC), Ave. Doctor Arce, 37, 28002 Madrid, Spain
| | - Melissabye Gunnoo
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94 T9PX, Ireland
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, (CSIC), Ave. Doctor Arce, 37, 28002 Madrid, Spain
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, PL-02668 Warsaw, Poland
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Unusually high mechanical stability of bacterial adhesin extender domains having calcium clamps. PLoS One 2017; 12:e0174682. [PMID: 28376122 PMCID: PMC5380327 DOI: 10.1371/journal.pone.0174682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/12/2017] [Indexed: 01/07/2023] Open
Abstract
To gain insight into the relationship between protein structure and mechanical stability, single molecule force spectroscopy experiments on proteins with diverse structure and topology are needed. Here, we measured the mechanical stability of extender domains of two bacterial adhesins MpAFP and MhLap, in an atomic force microscope. We find that both proteins are remarkably stable to pulling forces between their N- and C- terminal ends. At a pulling speed of 1 μm/s, the MpAFP extender domain fails at an unfolding force Fu = 348 ± 37 pN and MhLap at Fu = 306 ± 51 pN in buffer with 10 mM Ca2+. These forces place both extender domains well above the mechanical stability of many other β-sandwich domains in mechanostable proteins. We propose that the increased stability of MpAFP and MhLap is due to a combination of both hydrogen bonding between parallel terminal strands and intra-molecular coordination of calcium ions.
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39
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Poma AB, Cieplak M, Theodorakis PE. Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins. J Chem Theory Comput 2017; 13:1366-1374. [PMID: 28195464 DOI: 10.1021/acs.jctc.6b00986] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The application of coarse-grained (CG) models in biology is essential to access large length and time scales required for the description of many biological processes. The ELNEDIN protein model is based on the well-known MARTINI CG force-field and incorporates additionally harmonic bonds of a certain spring constant within a defined cutoff distance between pairs of residues, in order to preserve the native structure of the protein. In this case, the use of unbreakable harmonic bonds hinders the study of unfolding and folding processes. To overcome this barrier we have replaced the harmonic bonds with Lennard-Jones interactions based on the contact map of the native protein structure as is done in Go̅-like models. This model exhibits very good agreement with all-atom simulations and the ELNEDIN. Moreover, it can capture the structural motion linked to particular catalytic activity in the Man5B protein, in agreement with all-atom simulations. In addition, our model is based on the van der Waals radii, instead of a cutoff distance, which results in a smaller contact map. In conclusion, we anticipate that our model will provide further possibilities for studying biological systems based on the MARTINI CG force-field by using advanced-sampling methods, such as parallel tempering and metadynamics.
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Affiliation(s)
- Adolfo B Poma
- Institute of Physics, Polish Academy of Sciences , Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences , Al. Lotników 32/46, 02-668 Warsaw, Poland
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Artzi L, Bayer EA, Moraïs S. Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides. Nat Rev Microbiol 2017; 15:83-95. [PMID: 27941816 DOI: 10.1038/nrmicro.2016.164] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellulosomes are multienzyme complexes that are produced by anaerobic cellulolytic bacteria for the degradation of lignocellulosic biomass. They comprise a complex of scaffoldin, which is the structural subunit, and various enzymatic subunits. The intersubunit interactions in these multienzyme complexes are mediated by cohesin and dockerin modules. Cellulosome-producing bacteria have been isolated from a large variety of environments, which reflects their prevalence and the importance of this microbial enzymatic strategy. In a given species, cellulosomes exhibit intrinsic heterogeneity, and between species there is a broad diversity in the composition and configuration of cellulosomes. With the development of modern technologies, such as genomics and proteomics, the full protein content of cellulosomes and their expression levels can now be assessed and the regulatory mechanisms identified. Owing to their highly efficient organization and hydrolytic activity, cellulosomes hold immense potential for application in the degradation of biomass and are the focus of much effort to engineer an ideal microorganism for the conversion of lignocellulose to valuable products, such as biofuels.
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Affiliation(s)
- Lior Artzi
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
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41
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He C, Li H. Staphylokinase Displays Surprisingly Low Mechanical Stability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:1077-1083. [PMID: 28040904 DOI: 10.1021/acs.langmuir.6b04425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations have revealed that shear topology is an important structural feature for mechanically stable proteins. Proteins containing a β-grasp fold display the typical shear topology and are generally of significant mechanical stability. In an effort to experimentally identify mechanically strong proteins using single-molecule atomic force microscopy, we found that staphylokinase (SAK), which has a typical β-grasp fold and was predicted to be mechanically stable in coarse-grained MD simulations, displays surprisingly low mechanical stability. At a pulling speed of 400 nm/s, SAK unfolds at ∼60 pN, making it the mechanically weakest protein among the β-grasp fold proteins that have been characterized experimentally. In contrast, its structural homologous protein streptokinase β domain displays significant mechanical stability under the same experimental condition. Our results showed that the large malleability of native-state SAK is largely responsible for its low mechanical stability. The molecular origin of this large malleability of SAK remains unknown. Our results reveal a hidden complexity in protein mechanics and call for a detailed investigation into the molecular determinants of the protein mechanical malleability.
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Affiliation(s)
- Chengzhi He
- Department of Chemistry, University of British Columbia , Vancouver, BC V6T 1Z1, Canada
| | - Hongbin Li
- Department of Chemistry, University of British Columbia , Vancouver, BC V6T 1Z1, Canada
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42
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Topological transformations in proteins: effects of heating and proximity of an interface. Sci Rep 2017; 7:39851. [PMID: 28051124 PMCID: PMC5209716 DOI: 10.1038/srep39851] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/28/2016] [Indexed: 01/04/2023] Open
Abstract
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally distinct from those identified for folding at its optimal temperature. In particular, for shallowly knotted proteins, folding usually involves formation of two loops whereas unfolding through high-temperature heating is dominated by untying of single loops. Untying the knots is found to generally precede unfolding unless the protein is deeply knotted and the heating temperature exceeds a threshold value. We then use a phenomenological model of the air-water interface to show that such an interface can untie shallow knots, but it can also make knots in proteins that are natively unknotted.
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43
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Single-molecule force spectroscopy on polyproteins and receptor–ligand complexes: The current toolbox. J Struct Biol 2017; 197:3-12. [DOI: 10.1016/j.jsb.2016.02.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 11/21/2022]
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44
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Wojciechowski M, Cieplak M. Dual binding mode in cohesin-dockerin complexes as assessed through stretching studies. J Chem Phys 2016; 145:134102. [PMID: 27782410 DOI: 10.1063/1.4963693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A recent experimental study by Jobst et al. of stretching of a wild-type (WT) cohesin-dockerin complex has identified two kinds of the force-displacement patterns, with a single or double-peaked final rupture, which are termed "short" and "long" here. This duality has been interpreted as arising from the existence of two kinds of binding. Here, we analyze the separation of two cohesin-dockerin complexes of C. thermocellum theoretically. We use a coarse-grained structure-based model and the values of the pulling speeds are nearly experimental. In their native states, the two systems differ in the mutual binding orientations of the molecules in the complex. We demonstrate that the WT complex (PDB:1OHZ) unravels along two possible pathways that are qualitatively consistent with the presence of the short and long patterns observed experimentally. On the other hand, the mutated complex (PDB:2CCL) leads only to short trajectories. The short and long stretching pathways also appear in the cohesin-dockerin-Xmodule complex (PDB:4IU3, WT) of R. flavefaciens. Thus the duality in the stretching patterns need not be necessarily due to the duality in binding.
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Affiliation(s)
- Michał Wojciechowski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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45
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Nash MA, Smith SP, Fontes CM, Bayer EA. Single versus dual-binding conformations in cellulosomal cohesin-dockerin complexes. Curr Opin Struct Biol 2016; 40:89-96. [PMID: 27579515 DOI: 10.1016/j.sbi.2016.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/22/2016] [Accepted: 08/02/2016] [Indexed: 12/24/2022]
Abstract
Cohesins and dockerins are complementary interacting protein modules that form stable and highly specific receptor-ligand complexes. They play a crucial role in the assembly of cellulose-degrading multi-enzyme complexes called cellulosomes and have potential applicability in several technology areas, including biomass conversion processes. Here, we describe several exceptional properties of cohesin-dockerin complexes, including their tenacious biochemical affinity, remarkably high mechanostability and a dual-binding mode of recognition that is contrary to the conventional lock-and-key model of receptor-ligand interactions. We focus on structural aspects of the dual mode of cohesin-dockerin binding, highlighting recent single-molecule analysis techniques for its explicit characterization.
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Affiliation(s)
- Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany; Department of Chemistry, University of Basel, 4056 Basel, Switzerland; Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH-Zürich), 4058 Basel, Switzerland.
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Carlos Mga Fontes
- CIISA-Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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46
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Wołek K, Gómez-Sicilia À, Cieplak M. Determination of contact maps in proteins: A combination of structural and chemical approaches. J Chem Phys 2016; 143:243105. [PMID: 26723590 DOI: 10.1063/1.4929599] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones - a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.
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Affiliation(s)
- Karol Wołek
- Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Àngel Gómez-Sicilia
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid, Spain
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw, Poland
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47
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Gunnoo M, Cazade PA, Galera-Prat A, Nash MA, Czjzek M, Cieplak M, Alvarez B, Aguilar M, Karpol A, Gaub H, Carrión-Vázquez M, Bayer EA, Thompson D. Nanoscale Engineering of Designer Cellulosomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5619-47. [PMID: 26748482 DOI: 10.1002/adma.201503948] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/01/2015] [Indexed: 05/27/2023]
Abstract
Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.
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Affiliation(s)
- Melissabye Gunnoo
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Pierre-André Cazade
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Albert Galera-Prat
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC, Université Paris 06, and Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique, de Roscoff, CS 90074, F-29688, Roscoff cedex, Bretagne, France
| | - Marek Cieplak
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Beatriz Alvarez
- Biopolis S.L., Parc Científic de la Universitat de Valencia, Edificio 2, C/Catedrático Agustín Escardino 9, 46980, Paterna (Valencia), Spain
| | - Marina Aguilar
- Abengoa, S.A., Palmas Altas, Calle Energía Solar nº 1, 41014, Seville, Spain
| | - Alon Karpol
- Designer Energy Ltd., 2 Bergman St., Tamar Science Park, Rehovot, 7670504, Israel
| | - Hermann Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-University, 80799, Munich, Germany
| | - Mariano Carrión-Vázquez
- Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), IMDEA Nanociencias and CIBERNED, Madrid, Spain
| | - Edward A Bayer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Damien Thompson
- Materials and Surface Science Institute and Department of Physics and Energy, University of Limerick, Limerick, Ireland
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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]
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49
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CnaA domains in bacterial pili are efficient dissipaters of large mechanical shocks. Proc Natl Acad Sci U S A 2016; 113:2490-5. [PMID: 26884173 DOI: 10.1073/pnas.1522946113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Pathogenic bacteria adhere despite severe mechanical perturbations induced by the host, such as coughing. In Gram-positive bacteria, extracellular protein appendages termed pili are necessary for adherence under mechanical stress. However, little is known about the behavior of Gram-positive pili under force. Here, we demonstrate a mechanism by which Gram-positive pili are able to dissipate mechanical energy through mechanical unfolding and refolding of isopeptide bond-delimited polypeptide loops present in Ig-type CnaA domains. Using single-molecule force spectroscopy, we find that these loops of the pilus subunit SpaA of the SpaA-type pilus from Corynebacterium diphtheriae and FimA of the type 2 pilus from Actinomyces oris unfold and extend at forces that are the highest yet reported for globular proteins. Loop refolding is limited by the hydrophobic collapse of the polypeptide and occurs in milliseconds. Remarkably, both SpaA and FimA initially refold to mechanically weaker intermediates that recover strength with time or ligand binding. Based on the high force extensibility, CnaA-containing pili can dissipate ∼28-fold as much energy compared with their inextensible counterparts before reaching forces sufficient to cleave covalent bonds. We propose that efficient mechanical energy dissipation is key for sustained bacterial attachment against mechanical perturbations.
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50
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Kravats AN, Tonddast-Navaei S, Stan G. Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines. PLoS Comput Biol 2016; 12:e1004675. [PMID: 26734937 PMCID: PMC4703411 DOI: 10.1371/journal.pcbi.1004675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/25/2015] [Indexed: 01/30/2023] Open
Abstract
Clp ATPases are powerful ring shaped nanomachines which participate in the degradation pathway of the protein quality control system, coupling the energy from ATP hydrolysis to threading substrate proteins (SP) through their narrow central pore. Repetitive cycles of sequential intra-ring ATP hydrolysis events induce axial excursions of diaphragm-forming central pore loops that effect the application of mechanical forces onto SPs to promote unfolding and translocation. We perform Langevin dynamics simulations of a coarse-grained model of the ClpY ATPase-SP system to elucidate the molecular details of unfolding and translocation of an α/β model protein. We contrast this mechanism with our previous studies which used an all-α SP. We find conserved aspects of unfolding and translocation mechanisms by allosteric ClpY, including unfolding initiated at the tagged C-terminus and translocation via a power stroke mechanism. Topology-specific aspects include the time scales, the rate limiting steps in the degradation pathway, the effect of force directionality, and the translocase efficacy. Mechanisms of ClpY-assisted unfolding and translocation are distinct from those resulting from non-allosteric mechanical pulling. Bulk unfolding simulations, which mimic Atomic Force Microscopy-type pulling, reveal multiple unfolding pathways initiated at the C-terminus, N-terminus, or simultaneously from both termini. In a non-allosteric ClpY ATPase pore, mechanical pulling with constant velocity yields larger effective forces for SP unfolding, while pulling with constant force results in simultaneous unfolding and translocation. Cell survival is critically dependent on tightly regulated protein quality control, which includes chaperone-mediated folding and degradation. In the degradation pathway, AAA+ nanomachines, such as bacterial Clp proteases, use ATP-driven mechanisms to mechanically unfold, translocate, and destroy excess or defective proteins. Understanding these remodeling mechanisms is of central importance for deciphering the details of essential cellular processes. We perform coarse-grained computer simulations to extensively probe the effect of substrate protein topology on unfolding and translocation actions of the ClpY ATPase nanomachine. We find that, independent of SP topology, unfolding proceeds from the tagged C-terminus, which is engaged by the ATPase, and translocation involves coordinated steps. Topology-specific aspects include more complex unfolding and translocation pathways of the α/β SP compared with the all-α SP due to high stability of β-hairpins and interplay of tertiary contacts. In addition, directionality of the mechanical force applied by the Clp ATPase gives rise to distinct unfolding pathways.
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Affiliation(s)
- Andrea N. Kravats
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Sam Tonddast-Navaei
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
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