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Understanding the mechanism of amylin aggregation: From identifying crucial segments to tracing dominant sequential events to modeling potential aggregation suppressors. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140866. [PMID: 36272537 DOI: 10.1016/j.bbapap.2022.140866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022]
Abstract
One of the most abundant, prevailing, and life-threatening human diseases that are currently baffling the scientific community is type 2 diabetes (T2D). The self-association of human amylin has been implicated in the pathogenesis of T2D, though with an inconclusive understanding of the mechanism. Hence, we focused on the characterization of the conformational ensembles of all the species that are believed to define the structural polymorphism of the aggregation process - the functional monomeric, the initially self-associated oligomeric, and the structured protofibril - by employing near-equilibrium, non-equilibrium, and equilibrium atomistic simulations on the sporadic, two familial variants (S20G and G33R), and their proline-substituted forms (S20P and G33P). The dynamic near-equilibrium assays hint toward - the abundance of helical conformation in the monomeric state, the retainment of the helicity in the initial self-associated oligomeric phase pointing toward the existence of the helix-helix association mechanism, the difference in preference of specific segments to have definite secondary structural features, the phase-dependent variability in the dominance of specific segments and mutation sites, and the simultaneous presence of generic and unique features among various sequences. Furthermore, the non-equilibrium pulling assays exemplify a generic sequential unzipping mechanism of the protofibrils, however, the sequence-dependent uniqueness comes from the difference in location and magnitude of the control of a specific terminus. Importantly, the equilibrium thermodynamic assays efficiently rank order the potential of aggregability among sequences and consequently suggests the probability of designing effective aggregation suppressors against sporadic and familial amylin variants incorporating proline as the mutation.
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2
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Buell AK. Stability matters, too - the thermodynamics of amyloid fibril formation. Chem Sci 2022; 13:10177-10192. [PMID: 36277637 PMCID: PMC9473512 DOI: 10.1039/d1sc06782f] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/30/2022] [Indexed: 12/26/2022] Open
Abstract
Amyloid fibrils are supramolecular homopolymers of proteins that play important roles in biological functions and disease. These objects have received an exponential increase in attention during the last few decades, due to their role in the aetiology of a range of severe disorders, most notably some of a neurodegenerative nature. While an overwhelming number of experimental studies exist that investigate how, and how fast, amyloid fibrils form and how their formation can be inhibited, a much more limited body of experimental work attempts to answer the question as to why these types of structures form (i.e. the thermodynamic driving force) and how stable they actually are. In this review, I attempt to give an overview of the types of experiments that have been performed to-date to answer these questions, and to summarise our current understanding of amyloid thermodynamics.
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Affiliation(s)
- Alexander K Buell
- Technical University of Denmark, Department of Biotechnology and Biomedicine Søltofts Plads, Building 227 2800 Kgs. Lyngby Denmark
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3
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Vezenkov LT, Danalev DL, Iwanov I, Lozanov V, Atanasov A, Todorova R, Vassilev N, Karadjova V. Synthesis and biological study of new galanthamine-peptide derivatives designed for prevention and treatment of Alzheimer 's disease. Amino Acids 2022; 54:897-910. [PMID: 35562605 DOI: 10.1007/s00726-022-03167-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/23/2022] [Indexed: 11/29/2022]
Abstract
The Alzheimer's disease leads to neurodegenerative processes and affecting negatively million people worldwide. The treatment of the disease is still difficult and incomplete in practice. Galanthamine is one of the most commonly used drugs against the illness. The main aim of this work is design and synthesis of new derivatives of galanthamine comprising peptide moiety as well as study of their β-secretase inhibitory activity and the anti-aggregating effect. All new derivatives of galanthamine containing analogues of Leu-Val-Phe-Phe (Aβ17-Aβ20) were synthesized in solution using fragment and consecutive condensation approaches. The new derivatives were characterized by melting points, NMR, and HPLC/MS. They were tested in vitro for β-secretase inhibition activity by means of fluorescent method and were investigated in vitro for anti-aggregation activity on sheep platelet-rich plasma. Although the new compounds do not contain a structural element responsible for the β-secretase inhibition, five of them show high or good β-secretase inhibitory activity between 19.98 and 51.19% with IC50 between 1.95 and 5.26 nM. Four of the new molecules were able to inhibit platelet aggregation between 55.0 and 90.0% with IC50 between 0.69 and 1.36 µM. Four of the compounds were able to inhibit platelet aggregation and two of them have high anti-aggregating effects.
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Affiliation(s)
| | - Dancho L Danalev
- University of Chemical Technology and Metallurgy, Sofia, 1756, Bulgaria.
| | - Iwan Iwanov
- University of Chemical Technology and Metallurgy, Sofia, 1756, Bulgaria
| | - Valentin Lozanov
- Department of Medical Chemistry and Biochemistry, Medical University of Sofia, Sofia, 1000, Bulgaria
| | - Atanas Atanasov
- Medical Faculty, Trakia University, Stara Zagora, 6000, Bulgaria
| | - Rumyana Todorova
- Medical Faculty, Trakia University, Stara Zagora, 6000, Bulgaria
| | - Nikolay Vassilev
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
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Beaussart A, Canonico F, Mazon H, Hidalgo J, Cianférani S, Le Cordier H, Kriznik A, Rahuel-Clermont S. Probing the mechanism of the peroxiredoxin decamer interaction with its reductase sulfiredoxin from the single molecule to the solution scale. NANOSCALE HORIZONS 2022; 7:515-525. [PMID: 35234779 DOI: 10.1039/d2nh00037g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peroxiredoxins from the Prx1 subfamily (Prx) are highly regulated multifunctional proteins involved in oxidative stress response, redox signaling and cell protection. Prx is a homodimer that associates into a decamer. The monomer C-terminus plays intricate roles in Prx catalytic functions, decamer stability and interaction with its redox partner, the small reductase sulfiredoxin (Srx), that regulates the switching between Prx cellular functions. As only static structures of covalent Prx-Srx complexes have been reported, whether Srx binding dissociates the decameric assembly and how Prx subunit flexibility impacts complex formation are unknown. Here, we assessed the non-covalent interaction mechanism and dynamics in the solution of Saccharomyces cerevisiae Srx with the ten subunits of Prx Tsa1 at the decamer level via a combination of multiscale biophysical approaches including native mass spectrometry. We show that the ten subunits of the decamer can be saturated by ten Srx molecules and that the Tsa1 decamer in complex with Srx does not dissociate in solution. Furthermore, the binding events of atomic force microscopy (AFM) tip-grafted Srx molecules to Tsa1 individual subunits were relevant to the interactions between free molecules in solution. Combined with protein engineering and rapid kinetics, the observation of peculiar AFM force-distance signatures revealed that Tsa1 C-terminus flexibility controls Tsa1/Srx two-step binding and dynamics and determines the force-induced dissociation of Srx from each subunit of the decameric complex in a sequential or concerted mode. This combined approach from the solution to the single-molecule level offers promising prospects for understanding oligomeric protein interactions with their partners.
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Affiliation(s)
| | | | - Hortense Mazon
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Jorge Hidalgo
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087 Strasbourg, France
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
| | - Sophie Rahuel-Clermont
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
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5
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Plaut S. Scoping review and interpretation of myofascial pain/fibromyalgia syndrome: An attempt to assemble a medical puzzle. PLoS One 2022; 17:e0263087. [PMID: 35171940 PMCID: PMC8849503 DOI: 10.1371/journal.pone.0263087] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Myofascial Pain Syndrome (MPS) is a common, overlooked, and underdiagnosed condition and has significant burden. MPS is often dismissed by clinicians while patients remain in pain for years. MPS can evolve into fibromyalgia, however, effective treatments for both are lacking due to absence of a clear mechanism. Many studies focus on central sensitization. Therefore, the purpose of this scoping review is to systematically search cross-disciplinary empirical studies of MPS, focusing on mechanical aspects, and suggest an organic mechanism explaining how it might evolve into fibromyalgia. Hopefully, it will advance our understanding of this disease. METHODS Systematically searched multiple phrases in MEDLINE, EMBASE, COCHRANE, PEDro, and medRxiv, majority with no time limit. Inclusion/exclusion based on title and abstract, then full text inspection. Additional literature added on relevant side topics. Review follows PRISMA-ScR guidelines. PROSPERO yet to adapt registration for scoping reviews. FINDINGS 799 records included. Fascia can adapt to various states by reversibly changing biomechanical and physical properties. Trigger points, tension, and pain are a hallmark of MPS. Myofibroblasts play a role in sustained myofascial tension. Tension can propagate in fascia, possibly supporting a tensegrity framework. Movement and mechanical interventions treat and prevent MPS, while living sedentarily predisposes to MPS and recurrence. CONCLUSIONS MPS can be seen as a pathological state of imbalance in a natural process; manifesting from the inherent properties of the fascia, triggered by a disrupted biomechanical interplay. MPS might evolve into fibromyalgia through deranged myofibroblasts in connective tissue ("fascial armoring"). Movement is an underemployed requisite in modern lifestyle. Lifestyle is linked to pain and suffering. The mechanism of needling is suggested to be more mechanical than currently thought. A "global percutaneous needle fasciotomy" that respects tensegrity principles may treat MPS/fibromyalgia more effectively. "Functional-somatic syndromes" can be seen as one entity (myofibroblast-generated-tensegrity-tension), sharing a common rheuma-psycho-neurological mechanism.
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Affiliation(s)
- Shiloh Plaut
- School of Medicine, St. George’s University of London, London, United Kingdom
- * E-mail:
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Adhikari R, Yang M, Saikia N, Dutta C, Alharbi WFA, Shan Z, Pandey R, Tiwari A. Acetylation of Aβ42 at Lysine 16 Disrupts Amyloid Formation. ACS Chem Neurosci 2020; 11:1178-1191. [PMID: 32207962 PMCID: PMC7605495 DOI: 10.1021/acschemneuro.0c00069] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The residue lysine 28 (K28) is known to form an important salt bridge that stabilizes the Aβ amyloid structure, and acetylation of lysine 28 (K28Ac) slows the Aβ42 fibrillization rate but does not affect fibril morphology. On the other hand, acetylation of lysine 16 (K16Ac) residue greatly diminishes the fibrillization property of Aβ42 peptide and also affects its toxicity. This is due to the fact that lysine 16 acetylated amyloid beta peptide forms amorphous aggregates instead of amyloid fibrils. This is likely a result of increased hydrophobicity of the K16-A21 region due to K16 acetylation, as confirmed by molecular dynamic simulation studies. The calculated results show that the hydrophobic patches of aggregates from acetylated peptides were different when compared to wild-type (WT) peptide. K16Ac and double acetylated (KKAc) peptide aggregates show significantly higher cytotoxicity compared to the WT or K28Ac peptide aggregates alone. However, the heterogeneous mixture of WT and acetylated Aβ42 peptide aggregates exhibited higher free radical formation as well as cytotoxicity, suggesting dynamic interactions between different species could be a critical contributor to Aβ pathology.
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Affiliation(s)
- Rashmi Adhikari
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Mu Yang
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nabanita Saikia
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Colina Dutta
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Wafa F A Alharbi
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Zhiying Shan
- Department of Kinesiology and Integrative Physiology, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ravindra Pandey
- Department of Physics, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Ashutosh Tiwari
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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7
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Nanomechanical properties of steric zipper globular structures. Proc Natl Acad Sci U S A 2019; 116:22478-22484. [PMID: 31636220 DOI: 10.1073/pnas.1908782116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The term amyloid defines a group of proteins that aggregate into plaques or fibers. Amyloid fibers gained their fame mostly due to their relation with neurodegenerative diseases in humans. However, secreted by lower organisms, such as bacteria and fungi, amyloid fibers play a functional role: for example, when they serve as cement in the extracellular matrix of biofilms. Originating either in humans or in microorganisms, the sequence of amyloid proteins is decorated with hexapeptides with high propensity to form fibers, known as steric zippers. We have found that steric zippers form globular structures on route to making fibers and exhibit a characteristic force-distance (F-D) fingerprint when pulled with an atomic force microscope (AFM) tip. Particularly, the F-D pulling curves showed force plateau steps, suggesting that the globular structures were composed of chains that were unwound like a yarn ball. Force plateau analysis showed that the F-D characteristic parameters were sequence sensitive, representing differences in the packing of the hexapeptides within the globules. These unprecedented findings show that steric zippers exhibit a characteristic nanomechanical signature in solution in addition to previously observed characteristic crystallographic structure. Getting to the fundamental interactions that govern the unzipping of full-length amyloid fibers may initiate the development of antiamyloid methods that target the physical in addition to the structural properties of steric zippers.
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8
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Khan JM, Malik A, Rehman T, AlAjmi MF, Alamery SF, Alghamdi OHA, Khan RH, Odeibat HAM, Fatima S. Alpha-cyclodextrin turns SDS-induced amyloid fibril into native-like structure. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Delparastan P, Malollari KG, Lee H, Messersmith PB. Direct Evidence for the Polymeric Nature of Polydopamine. Angew Chem Int Ed Engl 2019; 58:1077-1082. [PMID: 30485624 PMCID: PMC6424361 DOI: 10.1002/anie.201811763] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/18/2018] [Indexed: 11/07/2022]
Abstract
Inspired by the adhesive proteins of mussels, polydopamine (pDA) has emerged as one of the most widely employed materials for surface functionalization. Despite numerous attempts at characterization, little consensus has emerged regarding whether pDA is a covalent polymer or a noncovalent aggregate of low molecular weight species. Here, we employed single-molecule force spectroscopy (SMFS) to characterize pDA films. Retraction of a pDA-coated cantilever from an oxide surface shows the characteristic features of a polymer with contour lengths of up to 200 nm. pDA polymers are generally weakly bound to the surface through much of their contour length, with occasional "sticky" points. Our findings represent the first direct evidence for the polymeric nature of pDA and provide a foundation upon which to better understand and tailor its physicochemical properties.
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Affiliation(s)
- Peyman Delparastan
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, 94720-1760 (USA),
| | | | - Haeshin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Phillip B. Messersmith
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, 94720-1760 (USA),
- Department of Bioengineering, University of California, Berkeley and Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley
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10
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Delparastan P, Malollari KG, Lee H, Messersmith PB. Direct Evidence for the Polymeric Nature of Polydopamine. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811763] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Peyman Delparastan
- Department of Materials Science and EngineeringUniversity of California, Berkeley Berkeley CA 94720-1760 USA
| | | | - Haeshin Lee
- Department of ChemistryKorea Advanced Institute of Science and Technology (KAIST) Daejeon South Korea
| | - Phillip B. Messersmith
- Department of Materials Science and EngineeringUniversity of California, Berkeley Berkeley CA 94720-1760 USA
- Department of BioengineeringUniversity of California Berkeley USA
- Materials Science DivisionLawrence Berkeley National Laboratory, Berkeley USA
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11
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Identification and nanomechanical characterization of the fundamental single-strand protofilaments of amyloid α-synuclein fibrils. Proc Natl Acad Sci U S A 2018; 115:7230-7235. [PMID: 29941606 PMCID: PMC6048494 DOI: 10.1073/pnas.1721220115] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The formation and spreading of amyloid aggregates from the presynaptic protein α-synuclein in the brain play central roles in the pathogenesis of Parkinson's disease. Here, we use high-resolution atomic force microscopy to investigate the early oligomerization events of α-synuclein with single monomer angstrom resolution. We identify, visualize, and characterize directly the smallest elementary unit in the hierarchical assembly of amyloid fibrils, termed here single-strand protofilaments. We show that protofilaments form from the direct molecular assembly of unfolded monomeric α-synuclein polypeptide chains. To unravel protofilaments' internal structure and elastic properties, we manipulated nanomechanically these species by atomic force spectroscopy. The single-molecule scale identification and characterization of the fundamental unit of amyloid assemblies provide insights into early events underlying their formation and shed light on opportunities for therapeutic intervention at the early stages of aberrant protein self-assembly.
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12
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Loveday SM, Gunning AP. Nanomechanics of Pectin-Linked β-Lactoglobulin Nanofibril Bundles. Biomacromolecules 2018; 19:2834-2840. [DOI: 10.1021/acs.biomac.8b00408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon M. Loveday
- Food and Bio-based
Products Group, AgResearch Limited, Private Bag 11008, Palmerston North, 4442, New Zealand
- Riddet Institute Centre of Research Excellence, Massey University, Palmerston North 4442, New Zealand
| | - A. Patrick Gunning
- Quadram Institute Bioscience, Norwich Research
Park, Norwich, Norfolk NR4 7UA, U.K
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13
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Prystopiuk V, Feuillie C, Herman-Bausier P, Viela F, Alsteens D, Pietrocola G, Speziale P, Dufrêne YF. Mechanical Forces Guiding Staphylococcus aureus Cellular Invasion. ACS NANO 2018; 12:3609-3622. [PMID: 29633832 DOI: 10.1021/acsnano.8b00716] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Staphylococcus aureus can invade various types of mammalian cells, thereby enabling it to evade host immune defenses and antibiotics. The current model for cellular invasion involves the interaction between the bacterial cell surface located fibronectin (Fn)-binding proteins (FnBPA and FnBPB) and the α5β1 integrin in the host cell membrane. While it is believed that the extracellular matrix protein Fn serves as a bridging molecule between FnBPs and integrins, the fundamental forces involved are not known. Using single-cell and single-molecule experiments, we unravel the molecular forces guiding S. aureus cellular invasion, focusing on the prototypical three-component FnBPA-Fn-integrin interaction. We show that FnBPA mediates bacterial adhesion to soluble Fn via strong forces (∼1500 pN), consistent with a high-affinity tandem β-zipper, and that the FnBPA-Fn complex further binds to immobilized α5β1 integrins with a strength much higher than that of the classical Fn-integrin bond (∼100 pN). The high mechanical stability of the Fn bridge favors an invasion model in which Fn binding by FnBPA leads to the exposure of cryptic integrin-binding sites via allosteric activation, which in turn engage in a strong interaction with integrins. This activation mechanism emphasizes the importance of protein mechanobiology in regulating bacterial-host adhesion. We also find that Fn-dependent adhesion between S. aureus and endothelial cells strengthens with time, suggesting that internalization occurs within a few minutes. Collectively, our results provide a molecular foundation for the ability of FnBPA to trigger host cell invasion by S. aureus and offer promising prospects for the development of therapeutic approaches against intracellular pathogens.
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Affiliation(s)
- Valeria Prystopiuk
- Institute of Life Sciences , Université catholique de Louvain , Croix du Sud, 4-5, bte L7.07.06 , B-1348 Louvain-la-Neuve , Belgium
| | - Cécile Feuillie
- Institute of Life Sciences , Université catholique de Louvain , Croix du Sud, 4-5, bte L7.07.06 , B-1348 Louvain-la-Neuve , Belgium
| | - Philippe Herman-Bausier
- Institute of Life Sciences , Université catholique de Louvain , Croix du Sud, 4-5, bte L7.07.06 , B-1348 Louvain-la-Neuve , Belgium
| | - Felipe Viela
- Institute of Life Sciences , Université catholique de Louvain , Croix du Sud, 4-5, bte L7.07.06 , B-1348 Louvain-la-Neuve , Belgium
| | - David Alsteens
- Institute of Life Sciences , Université catholique de Louvain , Croix du Sud, 4-5, bte L7.07.06 , B-1348 Louvain-la-Neuve , Belgium
| | | | | | - Yves F Dufrêne
- Institute of Life Sciences , Université catholique de Louvain , Croix du Sud, 4-5, bte L7.07.06 , B-1348 Louvain-la-Neuve , Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO) , 4000 Liège , Belgium
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14
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Ruggeri FS, Habchi J, Cerreta A, Dietler G. AFM-Based Single Molecule Techniques: Unraveling the Amyloid Pathogenic Species. Curr Pharm Des 2017; 22:3950-70. [PMID: 27189600 PMCID: PMC5080865 DOI: 10.2174/1381612822666160518141911] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/17/2016] [Indexed: 01/05/2023]
Abstract
Background A wide class of human diseases and neurodegenerative disorders, such as Alzheimer’s disease, is due to the failure of a specific peptide or protein to keep its native functional conformational state and to undergo a conformational change into a misfolded state, triggering the formation of fibrillar cross-β sheet amyloid aggregates. During the fibrillization, several coexisting species are formed, giving rise to a highly heterogeneous mixture. Despite its fundamental role in biological function and malfunction, the mechanism of protein self-assembly and the fundamental origins of the connection between aggregation, cellular toxicity and the biochemistry of neurodegeneration remains challenging to elucidate in molecular detail. In particular, the nature of the specific state of proteins that is most prone to cause cytotoxicity is not established. Methods: In the present review, we present the latest advances obtained by Atomic Force Microscopy (AFM) based techniques to unravel the biophysical properties of amyloid aggregates at the nanoscale. Unraveling amyloid single species biophysical properties still represents a formidable experimental challenge, mainly because of their nanoscale dimensions and heterogeneous nature. Bulk techniques, such as circular dichroism or infrared spectroscopy, are not able to characterize the heterogeneity and inner properties of amyloid aggregates at the single species level, preventing a profound investigation of the correlation between the biophysical properties and toxicity of the individual species. Conclusion: The information delivered by AFM based techniques could be central to study the aggregation pathway of proteins and to design molecules that could interfere with amyloid aggregation delaying the onset of misfolding diseases.
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Affiliation(s)
- Francesco Simone Ruggeri
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom.
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15
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Reinecke A, Bertinetti L, Fratzl P, Harrington MJ. Cooperative behavior of a sacrificial bond network and elastic framework in providing self-healing capacity in mussel byssal threads. J Struct Biol 2016; 196:329-339. [DOI: 10.1016/j.jsb.2016.07.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 12/13/2022]
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16
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Zinc-dependent mechanical properties of Staphylococcus aureus biofilm-forming surface protein SasG. Proc Natl Acad Sci U S A 2015; 113:410-5. [PMID: 26715750 DOI: 10.1073/pnas.1519265113] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Staphylococcus aureus surface protein SasG promotes cell-cell adhesion during the accumulation phase of biofilm formation, but the molecular basis of this interaction remains poorly understood. Here, we unravel the mechanical properties of SasG on the surface of living bacteria, that is, in its native cellular environment. Nanoscale multiparametric imaging of living bacteria reveals that Zn(2+) strongly increases cell wall rigidity and activates the adhesive function of SasG. Single-cell force measurements show that SasG mediates cell-cell adhesion via specific Zn(2+)-dependent homophilic bonds between β-sheet-rich G5-E domains on neighboring cells. The force required to unfold individual domains is remarkably strong, up to ∼500 pN, thus explaining how SasG can withstand physiological shear forces. We also observe that SasG forms homophilic bonds with the structurally related accumulation-associated protein of Staphylococcus epidermidis, suggesting the possibility of multispecies biofilms during host colonization and infection. Collectively, our findings support a model in which zinc plays a dual role in activating cell-cell adhesion: adsorption of zinc ions to the bacterial cell surface increases cell wall cohesion and favors the projection of elongated SasG proteins away from the cell surface, thereby enabling zinc-dependent homophilic bonds between opposing cells. This work demonstrates an unexpected relationship between mechanics and adhesion in a staphylococcal surface protein, which may represent a general mechanism among bacterial pathogens for activating cell association.
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17
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Trusova VM. Protein Fibrillar Nanopolymers: Molecular-Level Insights into Their Structural, Physical and Mechanical Properties. ACTA ACUST UNITED AC 2015. [DOI: 10.1142/s1793048015300029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Amyloid fibrils represent a generic class of mechanically strong and stable biomaterials with extremely advantageous properties. Although amyloids were initially associated only with severe neurological disorders, the role of these structures nowadays is shifting from health debilitating to highly beneficial both in biomedical and technological aspects. Intensive involvement of fibrillar assemblies into the wide range of pathogenic and functional processes strongly necessitate the molecular level characterization of the structural, physical and elastic features of protein nanofibrils. In the present contribution, we made an attempt to highlight the up-to-date progress in the understanding of amyloid properties from the polymer physics standpoint. The fundamental insights into protein fibril behavior are essential not only for development of therapeutic strategies to combat the protein misfolding disorders but also for rational and precise design of novel biodegradable protein-based nanopolymers.
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Affiliation(s)
- Valeriya M. Trusova
- Department of Nuclear and Medical Physics, V. N. Karazin Kharkiv National University, 4 Svobody Sq. Kharkiv 61072, Ukraine
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18
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Pletikapić G, Lannon H, Murvai Ü, Kellermayer MSZ, Svetličić V, Brujic J. Self-assembly of polysaccharides gives rise to distinct mechanical signatures in marine gels. Biophys J 2015; 107:355-364. [PMID: 25028877 DOI: 10.1016/j.bpj.2014.04.065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/10/2014] [Accepted: 04/28/2014] [Indexed: 12/13/2022] Open
Abstract
Marine-gel biopolymers were recently visualized at the molecular level using atomic force microscopy (AFM) to reveal fine fibril-forming networks with low to high degrees of cross-linking. In this work, we use force spectroscopy to quantify the intra- and intermolecular forces within the marine-gel network. Combining force measurements, AFM imaging, and the known chemical composition of marine gels allows us to identify the microscopic origins of distinct mechanical responses. At the single-fibril level, we uncover force-extension curves that resemble those of individual polysaccharide fibrils. They exhibit entropic elasticity followed by extensions associated with chair-to-boat transitions specific to the type of polysaccharide at high forces. Surprisingly, a low degree of cross-linking leads to sawtooth patterns that we attribute to the unraveling of polysaccharide entanglements. At a high degree of cross-linking, we observe force plateaus that arise from unzipping, as well as unwinding, of helical bundles. Finally, the complex 3D network structure gives rise to force staircases of increasing height that correspond to the hierarchical peeling of fibrils away from the junction zones. In addition, we show that these diverse mechanical responses also arise in reconstituted polysaccharide gels, which highlights their dominant role in the mechanical architecture of marine gels.
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Affiliation(s)
- G Pletikapić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - H Lannon
- Center for Soft Matter Research and Department of Physics, New York University, New York, New York
| | - Ü Murvai
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - M S Z Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - V Svetličić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - J Brujic
- Center for Soft Matter Research and Department of Physics, New York University, New York, New York.
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19
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Zaitsev BN, Benedetti F, Mikhaylov AG, Korneev DV, Sekatskii SK, Karakouz T, Belavin PA, Netesova NA, Protopopova EV, Konovalova SN, Dietler G, Loktev VB. Force-induced globule-coil transition in laminin binding protein and its role for viral-cell membrane fusion. J Mol Recognit 2015; 27:727-38. [PMID: 25319621 DOI: 10.1002/jmr.2399] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 05/21/2014] [Accepted: 05/27/2014] [Indexed: 12/16/2022]
Abstract
The specific interactions of the pairs laminin binding protein (LBP)-purified tick-borne encephalitis viral surface protein E and certain recombinant fragments of this protein, as well as West Nile viral surface protein E and certain recombinant fragments of that protein, are studied by combined methods of single-molecule dynamic force spectroscopy (SMDFS), enzyme immunoassay and optical surface waves-based biosensor measurements. The experiments were performed at neutral pH (7.4) and acid pH (5.3) conditions. The data obtained confirm the role of LBP as a cell receptor for two typical viral species of the Flavivirus genus. A comparison of these data with similar data obtained for another cell receptor of this family, namely human αVβ3 integrin, reveals that both these receptors are very important. Studying the specific interaction between the cell receptors in question and specially prepared monoclonal antibodies against them, we could show that both interaction sites involved in the process of virus-cell interaction remain intact at pH 5.3. At the same time, for these acid conditions characteristic for an endosome during flavivirus-cell membrane fusion, SMDFS data reveal the existence of a force-induced (effective already for forces as small as 30-70 pN) sharp globule-coil transition for LBP and LBP-fragments of protein E complexes. We argue that this conformational transformation, being an analog of abrupt first-order phase transition and having similarity with the famous Rayleigh hydrodynamic instability, might be indispensable for the flavivirus-cell membrane fusion process.
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Affiliation(s)
- Boris N Zaitsev
- Department of Molecular Virology for Flaviviruses and Viral Hepatitis, State Research Center for Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, 630559, Russia
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20
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Murvai Ü, Somkuti J, Smeller L, Penke B, Kellermayer MSZ. Structural and nanomechanical comparison of epitaxially and solution-grown amyloid β25-35 fibrils. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:327-32. [PMID: 25600136 DOI: 10.1016/j.bbapap.2015.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 12/28/2014] [Accepted: 01/11/2015] [Indexed: 11/30/2022]
Abstract
Aβ25-35, the fibril-forming, biologically active toxic fragment of the full-length amyloid β-peptide also forms fibrils on mica by an epitaxial assembly mechanism. Here we investigated, by using atomic force microscopy, nanomechanical manipulation and FTIR spectroscopy, whether the epitaxially grown fibrils display structural and mechanical features similar to the ones evolving under equilibrium conditions in bulk solution. Unlike epitaxially grown fibrils, solution-grown fibrils displayed a heterogeneous morphology and an apparently helical structure. While fibril assembly in solution occurred on a time scale of hours, it appeared within a few minutes on mica surface fibrils. Both types of fibrils showed a similar plateau-like nanomechanical response characterized by the appearance of force staircases. The IR spectra of both fibril types contained an intense peak between 1620 and 1640 cm(-1), indicating that β-sheets dominate their structure. A shift in the amide I band towards greater wave numbers in epitaxially assembled fibrils suggests that their structure is less compact than that of solution-grown fibrils. Thus, equilibrium conditions are required for a full structural compaction. Epitaxial Aβ25-35 fibril assembly, while significantly accelerated, may trap the fibrils in less compact configurations. Considering that under in vivo conditions the assembly of amyloid fibrils is influenced by the presence of extracellular matrix components, the ultimate fibril structure is likely to be influenced by the features of underlying matrix elements.
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Affiliation(s)
- Ünige Murvai
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094 Hungary
| | - Judit Somkuti
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094 Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094 Hungary
| | - Botond Penke
- Supramolecular and Nanostructured Materials Research Group of the Hungarian Academy of Sciences, Dóm tér 8, Szeged, H-6720,Hungary
| | - Miklós S Z Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, Budapest H-1094 Hungary; MTA-SE Molecular Biophysics Research Group, Semmelweis University, Tűzoltó u. 37-47, Budapest, Szeged, Dóm tér 81094 Hungary.
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21
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Volpatti LR, Knowles TPJ. Polymer physics inspired approaches for the study of the mechanical properties of amyloid fibrils. ACTA ACUST UNITED AC 2013. [DOI: 10.1002/polb.23428] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Lisa R. Volpatti
- Department of Chemistry; University of Cambridge; Lensfield Road, CB2 1EW United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry; University of Cambridge; Lensfield Road, CB2 1EW United Kingdom
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22
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Kellermayer MS, Murvai Ü, Horváth A, Lászlóffi E, Soós K, Penke B. Epitaxial assembly dynamics of mutant amyloid β25–35_N27C fibrils explored with time-resolved scanning force microscopy. Biophys Chem 2013; 184:54-61. [DOI: 10.1016/j.bpc.2013.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 08/28/2013] [Accepted: 08/28/2013] [Indexed: 11/26/2022]
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23
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Xu T, Lannon H, Wolf S, Nakamura F, Brujic J. Domain-domain interactions in filamin A (16-23) impose a hierarchy of unfolding forces. Biophys J 2013; 104:2022-30. [PMID: 23663845 DOI: 10.1016/j.bpj.2013.03.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/10/2013] [Accepted: 03/19/2013] [Indexed: 01/10/2023] Open
Abstract
The quaternary structure of Filamin A (FLNa) 16-23 was recently shown to exhibit multiple domain-domain interactions that lead to a propeller-like construction. Here we present single-molecule force spectroscopy experiments to show a wide variety of mechanical responses of this molecule and compare it with its linear counterpart FLNa 1-8. The compact structure of FLNa 16-23 leads to a broad distribution of rupture forces and end-to-end lengths in the force-extension mode and multiple unraveling timescales in the force-clamp mode. Moreover, a subset of force-extension trajectories reveals a mechanical hierarchy in which the rupture of domain-domain interactions at high forces (>200 pN) liberates the unfolding of individual domains at low forces (∼100 pN). This mechanism may also explain the order-of-magnitude difference in the rates of the biexponential fits to the distribution of unfolding dwell times under force-clamp. Overall, FLNa 16-23 under a force of 100 pN is more compliant than the linear FLNa 1-8. Because a physiological role of FLNa is to crosslink actin filaments, this range of responses allows it to accommodate a broad spectrum of forces exerted by the cell and its environment.
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Affiliation(s)
- Tianyou Xu
- Department of Physics and Center for Soft Matter Research, New York University, New York, New York, USA
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24
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Tripathi P, Beaussart A, Alsteens D, Dupres V, Claes I, von Ossowski I, de Vos WM, Palva A, Lebeer S, Vanderleyden J, Dufrêne YF. Adhesion and nanomechanics of pili from the probiotic Lactobacillus rhamnosus GG. ACS NANO 2013; 7:3685-3697. [PMID: 23531039 DOI: 10.1021/nn400705u] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Knowledge of the mechanisms by which bacterial pili adhere to host cells and withstand external forces is critical to our understanding of their functional roles and offers exciting avenues in biomedicine for controlling the adhesion of bacterial pathogens and probiotics. While much progress has been made in the nanoscale characterization of pili from Gram-negative bacteria, the adhesive and mechanical properties of Gram-positive bacterial pili remain largely unknown. Here, we use single-molecule atomic force microscopy to unravel the binding mechanism of pili from the probiotic Gram-positive bacterium Lactobacillus rhamnosus GG (LGG). First, we show that SpaC, the key adhesion protein of the LGG pilus, is a multifunctional adhesin with broad specificity. SpaC forms homophilic trans-interactions engaged in bacterial aggregation and specifically binds mucin and collagen, two major extracellular components of host epithelial layers. Homophilic and heterophilic interactions display similar binding strengths and dissociation rates. Next, pulling experiments on living bacteria demonstrate that LGG pili exhibit two unique mechanical responses, that is, zipper-like adhesion involving multiple SpaC molecules distributed along the pilus length and nanospring properties enabling pili to resist high force. These mechanical properties may represent a generic mechanism among Gram-positive bacterial pili for strengthening adhesion and withstanding shear stresses in the natural environment. The single-molecule experiments presented here may help us to design molecules capable of promoting or inhibiting bacterial-host interactions.
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Affiliation(s)
- Prachi Tripathi
- Institute of Life Sciences, Université catholique de Louvain, Croix du Sud, 1, bte L7.04.01, B-1348 Louvain-la-Neuve, Belgium
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25
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Hoffmann A, Neupane K, Woodside MT. Single-molecule assays for investigating protein misfolding and aggregation. Phys Chem Chem Phys 2013; 15:7934-48. [PMID: 23612887 DOI: 10.1039/c3cp44564j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein misfolding and aggregation are relevant to many fields. Recently, their investigation has experienced a revival as a central topic in the research of numerous human diseases, including Parkinson's and Alzheimer's. Much has been learned from ensemble biochemical approaches, but the inherently heterogeneous nature of the underlying processes has obscured many important details. Single-molecule techniques offer unique capabilities to study heterogeneous systems, while providing high temporal and structural resolution to characterize them. In this Perspective, we give an overview of the single-molecule assays that have been applied to protein misfolding and aggregation, which are mainly based on fluorescence and force spectroscopy. We describe some of the technical challenges involved in studying aggregation at the single-molecule level and discuss what has been learned about aggregation mechanisms from the different approaches.
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Affiliation(s)
- Armin Hoffmann
- Department of Physics, University of Alberta, Edmonton, AB, Canada
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27
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Nash MA, Gaub HE. Single-molecule adhesion of a stimuli-responsive oligo(ethylene glycol) copolymer to gold. ACS NANO 2012; 6:10735-10742. [PMID: 23113802 DOI: 10.1021/nn303963m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Adhesion of environmentally responsive polymers to biocompatible surfaces is an important issue that has been explored in several nanobiotechnology applications. Here, we prepared multi-responsive statistical copolymers of two oligo(ethylene glycol) methyl ether methacrylate macromonomers with differing ethylene glycol side chain lengths using RAFT polymerization. The lower critical solution temperature of the copolymers was characterized using visible light extinction, and the chemical composition and molecular weight were measured using NMR spectroscopy and size-exclusion chromatography, respectively. The characterization results demonstrated that the transition temperature could be controlled by varying the macromonomer feed ratios, and the molecular weight could be controlled by varying the amount of the RAFT chain transfer agent in the polymerization feed. Using AFM single-molecule force spectroscopy, we measured the adhesion characteristics of single copolymer molecules to a gold surface. We found that dehydration and collapse of the copolymer in a high ionic strength buffer resulted in dramatically reduced bridging length distributions that maintained their single-molecule bimodal character. In the collapsed state, the polymer exhibited a lower absolute desorption force while cooperativity effects were found to increase the desorption force per chain for multi-chain interactions. Our results confirmed that the polymer in a collapsed conformation exhibited a dramatically reduced volume occupancy above the gold surface. These results demonstrate at the single-molecule level how solvent-induced collapse of an environmentally responsive copolymer modulates surface adhesion forces and bridging length distributions in a controllable way.
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Affiliation(s)
- Michael A Nash
- Lehrstuhl für Angewandte Physik and Center for NanoScience, Ludwig-Maximilians-Universität, 80799 Munich, Germany.
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28
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Abstract
Bacterial and fungal species produce some of the best-characterized functional amyloids, that is, extracellular fibres that play key roles in mediating adhesion and biofilm formation. Yet, the molecular details underlying their mechanical strength remain poorly understood. Here, we use single-molecule atomic force microscopy to measure the mechanical properties of amyloids formed by Als cell adhesion proteins from the pathogen Candida albicans. We show that stretching Als proteins through their amyloid sequence yields characteristic force signatures corresponding to the mechanical unzipping of β-sheet interactions formed between surface-arrayed Als proteins. The unzipping probability increases with contact time, reflecting the time necessary for optimal inter β-strand associations. These results demonstrate that amyloid interactions provide cohesive strength to a major adhesion protein from a microbial pathogen, thereby strengthening cell adhesion. We suggest that such functional amyloids may represent a generic mechanism for providing mechanical strength to cell adhesion proteins. In nanotechnology, these single-molecule manipulation experiments provide new opportunities to understand the molecular mechanisms driving the cohesion of functional amyloid-based nanostructures.
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Affiliation(s)
- David Alsteens
- Universitê catholique de Louvain, Institute of Life Sciences & Institute of Condensed Matter and Nanosciences, Croix du Sud, 1, bte L7.04.01., B-1348 Louvain-la-Neuve, Belgium
| | - Caleen B. Ramsook
- Department of Biology, Brooklyn College of City University of New York, Brooklyn, New York 11210, USA
| | - Peter N. Lipke
- Department of Biology, Brooklyn College of City University of New York, Brooklyn, New York 11210, USA
- Corresponding authors: Yves Dufrêne: , Peter Lipke:
| | - Yves F. Dufrêne
- Universitê catholique de Louvain, Institute of Life Sciences & Institute of Condensed Matter and Nanosciences, Croix du Sud, 1, bte L7.04.01., B-1348 Louvain-la-Neuve, Belgium
- Corresponding authors: Yves Dufrêne: , Peter Lipke:
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29
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Sweers KKM, Bennink ML, Subramaniam V. Nanomechanical properties of single amyloid fibrils. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:243101. [PMID: 22585542 DOI: 10.1088/0953-8984/24/24/243101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Amyloid fibrils are traditionally associated with neurodegenerative diseases like Alzheimer's disease, Parkinson's disease or Creutzfeldt-Jakob disease. However, the ability to form amyloid fibrils appears to be a more generic property of proteins. While disease-related, or pathological, amyloid fibrils are relevant for understanding the pathology and course of the disease, functional amyloids are involved, for example, in the exceptionally strong adhesive properties of natural adhesives. Amyloid fibrils are thus becoming increasingly interesting as versatile nanobiomaterials for applications in biotechnology. In the last decade a number of studies have reported on the intriguing mechanical characteristics of amyloid fibrils. In most of these studies atomic force microscopy (AFM) and atomic force spectroscopy play a central role. AFM techniques make it possible to probe, at nanometer length scales, and with exquisite control over the applied forces, biological samples in different environmental conditions. In this review we describe the different AFM techniques used for probing mechanical properties of single amyloid fibrils on the nanoscale. An overview is given of the existing mechanical studies on amyloid. We discuss the difficulties encountered with respect to the small fibril sizes and polymorphic behavior of amyloid fibrils. In particular, the different conformational packing of monomers within the fibrils leads to a heterogeneity in mechanical properties. We conclude with a brief outlook on how our knowledge of these mechanical properties of the amyloid fibrils can be exploited in the construction of nanomaterials from amyloid fibrils.
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Affiliation(s)
- K K M Sweers
- Nanobiophysics, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands.
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30
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Lyubchenko YL, Krasnoslobodtsev AV, Luca S. Fibrillogenesis of huntingtin and other glutamine containing proteins. Subcell Biochem 2012; 65:225-51. [PMID: 23225006 PMCID: PMC4226413 DOI: 10.1007/978-94-007-5416-4_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This chapter focuses on the aggregation of glutamine containing peptides and proteins with an emphasis on huntingtin protein, whose aggregation leads to the development of Huntington's disease. The kinetics that leads to the formation of amyloids, the structure of aggregates of various types and the morphological mechanical properties of amyloid fibrils are described. The kinetics of amyloid fibril formation has been proposed to follow a nucleation dependent polymerization model, dependent upon the size of the nucleus. This model and the effect of the polyglutamine length on the nucleus size are reviewed. Aggregate structure is characterized at two different levels. The atomic-scale resolution structure of fibrillar and crystalline aggregates of polyglutamine containing proteins and peptides was determined by X-ray crystallography and solid-state nuclear magnetic resonance (NMR). The chapter outlines the results obtained by both these techniques. Atomic force microscopy (AFM) was instrumental in elucidating the morphology of fibrils, their organization and assembly. The chapter also discusses the high stability of amyloid fibrils, including their mechanical properties as revealed by AFM.
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Affiliation(s)
- Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Alexey V. Krasnoslobodtsev
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Sorin Luca
- Department of Pharmaceutical Sciences, Nanoimaging Core Facility College of Pharmacy, University of Nebraska Medical Center, COP 1012, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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31
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Pires RH, Saraiva MJ, Damas AM, Kellermayer MSZ. Structure and assembly-disassembly properties of wild-type transthyretin amyloid protofibrils observed with atomic force microscopy. J Mol Recognit 2011; 24:467-76. [PMID: 21504025 DOI: 10.1002/jmr.1112] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Transthyretin (TTR) is an important human transport protein present in the serum and the cerebrospinal fluid. Aggregation of TTR in the form of amyloid fibrils is associated with neurodegeneration, but the mechanisms of cytotoxicity are likely to stem from the presence of intermediate assembly states. Characterization of these intermediate species is therefore essential to understand the etiology and pathogenesis of TTR-related amyloidoses. In the present work we used atomic force microscopy to investigate the morphological features of wild-type (WT) TTR amyloid protofibrils that appear in the early stages of aggregation. TTR protofibrils obtained by mild acidification appeared as flexible filaments with variable length and were able to bind amyloid markers (thioflavin T and Congo red). Surface topology and contour-length distribution displayed a periodic pattern of ∼ 15 nm, suggesting that the protofibrils assemble via an end-binding oligomer fusion mechanism. The average height and periodic substructure found in protofibrils is compatible with the double-helical model of the TTR amyloid protofilament. Over time protofibrils aggregated into bundles and did not form mature amyloid-like fibrils. Unlike amyloid fibrils that are typically stable under physiological conditions, the bundles dissociated into component protofibrils with axially compacted and radially dilated structure when exposed to phosphate-buffered saline solution. Thus, WT TTR can form metastable filamentous aggregates that may represent an important transient state along the pathway towards the formation of cytotoxic TTR species.
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Affiliation(s)
- Ricardo H Pires
- Department of Biophysics and Radiation Biology, Faculty of Medicine, Semmelweis University, Tűzoltó u. 37-47, Budapest IX, H1094 Hungary.
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32
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Murvai Ü, Soós K, Penke B, Kellermayer MSZ. Effect of the beta-sheet-breaker peptide LPFFD on oriented network of amyloid β25-35 fibrils. J Mol Recognit 2011; 24:453-60. [DOI: 10.1002/jmr.1113] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Optical trapping with high forces reveals unexpected behaviors of prion fibrils. Nat Struct Mol Biol 2010; 17:1422-30. [PMID: 21113168 DOI: 10.1038/nsmb.1954] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 10/18/2010] [Indexed: 11/08/2022]
Abstract
Amyloid fibrils are important in diverse cellular functions, feature in many human diseases and have potential applications in nanotechnology. Here we describe methods that combine optical trapping and fluorescent imaging to characterize the forces that govern the integrity of amyloid fibrils formed by a yeast prion protein. A crucial advance was to use the self-templating properties of amyloidogenic proteins to tether prion fibrils, enabling their manipulation in the optical trap. At normal pulling forces the fibrils were impervious to disruption. At much higher forces (up to 250 pN), discontinuities occurred in force-extension traces before fibril rupture. Experiments with selective amyloid-disrupting agents and mutations demonstrated that such discontinuities were caused by the unfolding of individual subdomains. Thus, our results reveal unusually strong noncovalent intermolecular contacts that maintain fibril integrity even when individual monomers partially unfold and extend fibril length.
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Hashimoto M, Shahdat HM, Katakura M, Tanabe Y, Gamoh S, Miwa K, Shimada T, Shido O. Effects of docosahexaenoic acid on in vitro amyloid beta peptide 25–35 fibrillation. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:289-96. [DOI: 10.1016/j.bbalip.2009.01.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 12/22/2008] [Accepted: 01/16/2009] [Indexed: 10/21/2022]
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35
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Nanomechanical Characterization of the Triple β-Helix Domain in the Cell Puncture Needle of Bacteriophage T4 Virus. Cell Mol Bioeng 2009. [DOI: 10.1007/s12195-009-0047-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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36
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Bura E, Zhmurov A, Barsegov V. Nonparametric density estimation and optimal bandwidth selection for protein unfolding and unbinding data. J Chem Phys 2009; 130:015102. [DOI: 10.1063/1.3050095] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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37
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Keten S, Buehler MJ. Strength limit of entropic elasticity in beta-sheet protein domains. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:061913. [PMID: 19256874 DOI: 10.1103/physreve.78.061913] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Indexed: 05/27/2023]
Abstract
Elasticity and strength of individual beta-sheet protein domains govern key biological functions and the mechanical properties of biopolymers including spider silk, amyloids, and muscle fibers. The worm-like-chain (WLC) model is commonly used to describe the entropic elasticity of polypeptides and other biomolecules. However, force spectroscopy experiments have shown pronounced deviations from the ideal WLC behavior, leading to controversial views about the appropriate elastic description of proteins at nanoscale. Here we report a simple model that explains the physical mechanism that leads to the breakdown of the WLC idealization in experiments by using only two generic parameters of the protein domain, the H-bond energy and the protein backbone's persistence length. We show that a rupture initiation condition characterized by the free energy release rate of H-bonds characterizes the limit of WLC entropic elasticity of beta-sheet protein domains and the onset of rupture. Our findings reveal that strength and elasticity are coupled and cannot be treated separately. The predictions of the model are compared with atomic force microscopy experiments of protein rupture.
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Affiliation(s)
- Sinan Keten
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Room 1-235A&B, Cambridge, Massachusetts 02139, USA
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Rivière C, Delaunay JC, Immel F, Cullin C, Monti JP. The polyphenol piceid destabilizes preformed amyloid fibrils and oligomers in vitro: hypothesis on possible molecular mechanisms. Neurochem Res 2008; 34:1120-8. [PMID: 19030989 DOI: 10.1007/s11064-008-9883-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2008] [Indexed: 11/30/2022]
Abstract
Alzheimer's disease (AD) is characterized by deposits of amyloid in various tissues. The neuronal cytotoxicity of Abeta peptides is attributed not only to various mechanisms but also to amyloid fibrils and soluble oligomeric intermediates. Consequently, finding molecules to prevent or reverse the oligomerization and fibrillization of Abeta could be of therapeutic value in the treatment of AD. We show that piceid, a polyphenol of the stilbene family, destabilized fibrils and oligomers to give back monomers that are not neurotoxic molecules. The mechanism of this destabilization could be a dynamic interaction between the polyphenol and the Abeta that could open the hydrophobic zipper and shift the reversible equilibrium "random coil<-->beta-sheet" to the disordered structure.
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Affiliation(s)
- Céline Rivière
- Laboratoire de physique et biophysique, GESVAB EA 3675, ISVV, Université de Bordeaux 2, Bordeaux cedex, France
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39
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Wolf MG, Jongejan JA, Laman JD, de Leeuw SW. Quantitative Prediction of Amyloid Fibril Growth of Short Peptides from Simulations: Calculating Association Constants To Dissect Side Chain Importance. J Am Chem Soc 2008; 130:15772-3. [DOI: 10.1021/ja806606y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maarten G. Wolf
- Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Jaap A. Jongejan
- Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Jon D. Laman
- Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Simon W. de Leeuw
- Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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40
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Wolf MG, Jongejan JA, Laman JD, de Leeuw SW. Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling. J Phys Chem B 2008; 112:13493-8. [DOI: 10.1021/jp804285e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Maarten G. Wolf
- Delft University of Technology, Julianalaan 136, 2628 BL Delft, Netherlands, Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, Netherlands, and Theoretical Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Jaap A. Jongejan
- Delft University of Technology, Julianalaan 136, 2628 BL Delft, Netherlands, Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, Netherlands, and Theoretical Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Jon D. Laman
- Delft University of Technology, Julianalaan 136, 2628 BL Delft, Netherlands, Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, Netherlands, and Theoretical Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Simon W. de Leeuw
- Delft University of Technology, Julianalaan 136, 2628 BL Delft, Netherlands, Department of Immunology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, Netherlands, and Theoretical Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
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41
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Dong M, Hovgaard MB, Mamdouh W, Xu S, Otzen DE, Besenbacher F. AFM-based force spectroscopy measurements of mature amyloid fibrils of the peptide glucagon. NANOTECHNOLOGY 2008; 19:384013. [PMID: 21832572 DOI: 10.1088/0957-4484/19/38/384013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We report on the mechanical characterization of individual mature amyloid fibrils by atomic force microscopy (AFM) and AFM-based single-molecule force spectroscopy (SMFS). These self-assembling materials, formed from the 29-residue amphiphatic peptide hormone glucagon, were found to display a reversible elastic behaviour. Based on AFM morphology and SMFS studies, we suggest that the observed elasticity is due to a force-induced conformational transition which is reversible due to the β-helical conformation of protofibrils, allowing a high degree of extension. The elastic properties of such mature fibrils contribute to their high stability, suggesting that the internal hydrophobic interactions of amyloid fibrils are likely to be of fundamental importance in the assembly of amyloid fibrils and therefore for the understanding of the progression of their associated pathogenic disorders. In addition, such biological amyloid fibril structures with highly stable mechanical properties can potentially be used to produce nanofibres (nanowires) that may be suitable for nanotechnological applications.
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Affiliation(s)
- Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, DK-8000 Aarhus C, Denmark. Department of Physics and Astronomy, University of Aarhus, DK-8000 Aarhus C, Denmark
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42
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Concentration dependence of alpha-synuclein fibril length assessed by quantitative atomic force microscopy and statistical-mechanical theory. Biophys J 2008; 95:4871-8. [PMID: 18676659 DOI: 10.1529/biophysj.107.127464] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The initial concentration of monomeric amyloidogenic proteins is a crucial factor in the in vitro formation of amyloid fibrils. We use quantitative atomic force microscopy to study the effect of the initial concentration of human alpha-synuclein on the mean length of mature alpha-synuclein fibrils, which are associated with Parkinson's disease. We determine that the critical initial concentration, below which low-molecular-weight species dominate and above which fibrils are the dominant species, lies at approximately 15 muM, in good agreement with earlier measurements using biochemical methods. In the concentration regime where fibrils dominate, we find that their mean length increases with initial concentration. These results correspond well to the qualitative predictions of a recent statistical-mechanical model of amyloid fibril formation. In addition, good quantitative agreement of the statistical-mechanical model with the measured mean fibril length as a function of initial protein concentration, as well as with the fibril length distributions for several protein concentrations, is found for reasonable values of the relevant model parameters. The comparison between theory and experiment yields, for the first time to our knowledge, an estimate of the magnitude of the free energies associated with the intermolecular interactions that govern alpha-synuclein fibril formation.
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43
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Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 2008; 5:491-505. [PMID: 18511917 DOI: 10.1038/nmeth.1218] [Citation(s) in RCA: 1375] [Impact Index Per Article: 85.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.
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44
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Nanomechanical properties of human prion protein amyloid as probed by force spectroscopy. Biophys J 2008; 95:2909-15. [PMID: 18539633 DOI: 10.1529/biophysj.108.133108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Amyloids are associated with a number of protein misfolding disorders, including prion diseases. In this study, we used single-molecule force spectroscopy to characterize the nanomechanical properties and molecular structure of amyloid fibrils formed by human prion protein PrP90-231. Force-extension curves obtained by specific attachment of a gold-covered atomic force microscope tip to engineered Cys residues could be described by the worm-like chain model for entropic elasticity of a polymer chain, with the size of the N-terminal segment that could be stretched entropically depending on the tip attachment site. The data presented here provide direct information about the forces required to extract an individual monomer from the core of the PrP90-231 amyloid, and indicate that the beta-sheet core of this amyloid starts at residue approximately 164-169. The latter finding has important implications for the ongoing debate regarding the structure of PrP amyloid.
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45
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Chiovitti A, Heraud P, Dugdale TM, Hodson OM, Curtain RCA, Dagastine RR, Wood BR, Wetherbee R. Divalent cations stabilize the aggregation of sulfated in the adhesive nanofibers of the biofouling diatom Toxarium undulatum. SOFT MATTER 2008; 4:811-820. [PMID: 32907187 DOI: 10.1039/b715455k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A species of marine diatom, Toxarium undulatum, has emerged as a problematic biofouler of contemporary environmentally benign marine coatings. Previous analyses by atomic force microscopy (AFM) showed the cell-substratum adhesive of this alga contained macromolecules with a modular protein backbone assembled into nanofibers in which the domains of the macromolecules folded and unfolded in a co-ordinated manner. In the present study, we investigated further the composition and properties of the adhesive. A combination of energy dispersive X-ray analysis (EDXA) and Fourier transform infrared (FTIR) spectroscopy showed that the adhesive contained mainly protein, carbohydrate, sulfate, calcium, and magnesium. AFM demonstrated that EDTA treatment of native T. undulatum adhesive resulted in rapid disruption of the adhesive nanofiber (ANF) structure but ANFs were restored by subsequent treatment (within 1 h) with solutions containing divalent cations. Prolonged exposure to EDTA (≥18 h) led to cell detachment. The soluble EDTA extract was separated from the cells, dialyzed, concentrated, and analyzed further. The extract had a protein-to-carbohydrate-to-sulfate weight ratio of 1.0 : 0.2 : 0.9 and contained a single, high-molecular-mass (>220 kDa) band by SDS-PAGE which was visualized by Stains-All® but not by Coomassie blue, indicating that it was a highly anionic macromolecule. The most abundant amino acids in the extract were glycine (22 mol%), aspartic acid/aspartamine (14 mol%), and histidine (11 mol%). The adhesive contained 11 neutral sugars dominated by mannose (50 mol%) and xylose (29 mol%). On the basis of these data, we propose that the ANFs of T. undulatum are composed of sulfated high-molecular-mass glycoproteins cross-linked by calcium and magnesium ions. The cross-linking enables domains of adjacent protein backbones to unfold and re-fold in register.
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Affiliation(s)
- Anthony Chiovitti
- School of Botany, University of Melbourne, Victoria 3010, Australia.
| | - Philip Heraud
- Centre for Biospectroscopy, Monash University, Clayton, Victoria 3800, Australia
| | - Tony M Dugdale
- School of Botany, University of Melbourne, Victoria 3010, Australia.
| | - Oliver M Hodson
- School of Botany, University of Melbourne, Victoria 3010, Australia.
| | - Roger C A Curtain
- Department of Chemical and Biomolecular Engineering, University of Melbourne, Victoria 3010, Australia
| | - Raymond R Dagastine
- Department of Chemical and Biomolecular Engineering, University of Melbourne, Victoria 3010, Australia and Particulate Fluids Processing Centre, University of Melbourne, Victoria 3010, Australia
| | - Bayden R Wood
- Centre for Biospectroscopy, Monash University, Clayton, Victoria 3800, Australia
| | - Richard Wetherbee
- School of Botany, University of Melbourne, Victoria 3010, Australia.
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46
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Decker B, Kellermayer MSZ. Periodically arranged interactions within the myosin filament backbone revealed by mechanical unzipping. J Mol Biol 2008; 377:307-10. [PMID: 18262203 DOI: 10.1016/j.jmb.2008.01.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/06/2008] [Accepted: 01/08/2008] [Indexed: 11/30/2022]
Abstract
Numerous types of biological motion are driven by myosin thick filaments. Although the exact structure of the filament backbone is not known, it has long been hypothesized that periodically arranged charged regions along the myosin tail are the main contributors to filament stability. Here we provide a direct experimental test of this model by mechanically pulling apart synthetic myosin thick filaments. We find that unzipping is accompanied by broad force peaks periodically spaced at 4-, 14- and 43-nm intervals. This spacing correlates with the repeat distance of highly charged regions along the myosin tail. Lowering ionic strength does not change force-peak periodicity but increases the forces necessary for unzipping. The force peaks are partially reversible, indicating that the interactions are rapidly re-established upon mechanical relaxation. Thus, the zipping together of myosin tails via consecutive formation of periodically spaced bonds may be the underlying mechanism of spontaneous thick filament formation.
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Affiliation(s)
- Brennan Decker
- Department of Biophysics, University of Pécs, Faculty of Medicine, Szigeti u. 12, Pécs H-7624, Hungary
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47
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Oriented epitaxial growth of amyloid fibrils of the N27C mutant beta 25-35 peptide. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:1133-7. [PMID: 18189132 DOI: 10.1007/s00249-007-0253-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 12/07/2007] [Accepted: 12/13/2007] [Indexed: 10/22/2022]
Abstract
Amyloid fibrils are present in the extracellular space of various tissues in neurodegenerative and protein misfolding diseases. Amyloid fibrils may be used in nanotechnology applications, because of their self-assembly properties and stability, if their growth and orientation can be controlled. Recently, we have shown that amyloid beta 25-35 (A beta 25-35) forms a highly oriented, K(+)-dependent network on mica. Here, we analyzed the properties of A beta 25-35_N27C, the cysteine residue of which may be used for subsequent chemical modifications. We find that A beta 25-35_N27C forms epitaxially growing fibrils on mica, which evolve into a trigonally oriented branched network. The binding is apparently more sensitive to cation concentration than that of the wild-type peptide. By nanomanipulating A beta 25-35_N27C fibrils with a gold-coated AFM tip, we show that the sulfhydryl of Cys27 is reactive and accessible from the solution. The oriented network of A beta 25-35_N27C fibrils can therefore be specifically labeled and may be used for constructing nanobiotechnological devices.
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Abstract
Amyloid fibrils are structures consisting of many proteins with a well-defined conformation. The formation of these fibrils has been the subject of intense research, largely due to their connection to several diseases. We focus here on the computational studies and discuss these from a free-energy point of view. The fibrillogenic properties of many proteins can be predicted and understood by taking the relevant free energies into account in an appropriate way. This is because both the equilibrium and the kinetic properties of the protein system depend on its free-energy landscape. Advanced simulation techniques can be used to understand the relationship between the free-energy landscape of a protein and its three-dimensional structure and propensity to form amyloid fibrils. We give an overview of existing simulation techniques that operate at a molecular level of detail and that are capable of generating relevant free-energy values. The free energies obtained with these methods can be inserted into a statistical-mechanical or kinetic framework to predict mean fibril properties on length scales and time scales that are inaccessible by molecular-scale simulation methods.
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Affiliation(s)
- Maarten G Wolf
- DelftChemTech, Delft University of Technology, Delft, The Netherlands
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49
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Raman EP, Takeda T, Barsegov V, Klimov DK. Mechanical unbinding of abeta peptides from amyloid fibrils. J Mol Biol 2007; 373:785-800. [PMID: 17868685 DOI: 10.1016/j.jmb.2007.08.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2007] [Revised: 08/08/2007] [Accepted: 08/13/2007] [Indexed: 10/22/2022]
Abstract
Using the experimental structures of Abeta amyloid fibrils and all-atom molecular dynamics, we study the force-induced unbinding of Abeta peptides from the fibril. We show that the mechanical dissociation of Abeta peptides is highly anisotropic and proceeds via different pathways when force is applied in parallel or perpendicular direction with respect to the fibril axis. The threshold forces associated with lateral unbinding of Abeta peptides exceed those observed during the mechanical dissociation along the fibril axis. In addition, Abeta fibrils are found to be brittle in the lateral direction of unbinding and soft along the fibril axis. Lateral mechanical unbinding and the unbinding along the fibril axis load different types of fibril interactions. Lateral unbinding is primarily determined by the cooperative rupture of fibril backbone hydrogen bonds. The unbinding along the fibril axis largely depends on the interpeptide Lys-Asp electrostatic contacts and the hydrophobic interactions formed by the Abeta C terminal. Due to universality of the amyloid beta structure, the anisotropic mechanical dissociation observed for Abeta fibrils is likely to be applicable to other amyloid assemblies. The estimates of equilibrium forces required to dissociate Abeta peptide from the amyloid fibril suggest that these supramolecular structures are mechanically stronger than most protein domains.
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Affiliation(s)
- E Prabhu Raman
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA 20110, USA
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50
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Kransnoslobodtsev AV, Shlyakhtenko LS, Ukraintsev E, Zaikova TO, Keana JF, Lyubchenko YL. Nanomedicine and protein misfolding diseases. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2007; 1:300-5. [PMID: 16467913 PMCID: PMC1351038 DOI: 10.1016/j.nano.2005.10.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Misfolding and self assembly of proteins in nano-aggregates of different sizes and morphologies (nano-ensembles, primarily nanofilaments and nano-rings) is a complex phenomenon that can be facilitated, impeded, or prevented, by interactions with various intracellular metabolites, intracellular nanomachines controlling protein folding and interactions with other proteins. A fundamental understanding of molecular processes leading to misfolding and self-aggregation of proteins involved in various neurodegenerative diseases will provide critical information to help identify appropriate therapeutic routes to control these processes. An elevated propensity of misfolded protein conformation in solution to aggregate with the formation of various morphologies impedes the use of traditional physical chemical approaches for studies of misfolded conformations of proteins. In our recent alternative approach, the protein molecules were tethered to surfaces to prevent aggregation and AFM force spectroscopy was used to probe the interaction between protein molecules depending on their conformations. It was shown that formation of filamentous aggregates is facilitated at pH values corresponding to the maximum of rupture forces. In this paper, a novel surface chemistry was developed for anchoring of amyloid beta (Abeta) peptides at their N-terminal moieties. The use of the site specific immobilization procedure allowed to measure the rupture of Abeta-Abeta contacts at single molecule level. The rupture of these contacts is accompanied by the extension of the peptide chain detected by a characteristic elasto-mechanical component of the force-distance curves. Potential applications of the nanomechanical studies to understanding the mechanisms of development of protein misfolding diseases are discussed.
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Affiliation(s)
| | - Luda S. Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198
| | - Egor Ukraintsev
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198
| | - Tatiana O. Zaikova
- Department of Chemistry, 1253 University of Oregon, Eugene, OR 97403-1253
| | - John F.W. Keana
- Department of Chemistry, 1253 University of Oregon, Eugene, OR 97403-1253
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198
- *Corresponding author: Yuri Lyubchenko, Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, Phone: 402-559-1971 – office, 402-559-1973 - lab 1, 402-559-1974 - lab 2, Fax: 402-559-9543, E-mail:
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