1
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Broderick TL, Rasool S, Li R, Zhang Y, Anderson M, Al-Nakkash L, Plochocki JH, Geetha T, Babu JR. Neuroprotective Effects of Chronic Resveratrol Treatment and Exercise Training in the 3xTg-AD Mouse Model of Alzheimer's Disease. Int J Mol Sci 2020; 21:ijms21197337. [PMID: 33020412 PMCID: PMC7582460 DOI: 10.3390/ijms21197337] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
To date, there is no cure or effective treatment for Alzheimer’s disease (AD), a chronic neurodegenerative condition that affects memory, language, and behavior. AD is characterized by neuroinflammation, accumulation of brain amyloid-beta (Aβ) oligomers and neurofibrillary tangles, increased neuronal apoptosis, and loss of synaptic function. Promoting regular exercise and a diet containing polyphenols are effective non-pharmacological approaches that prevent the progression of neurodegenerative diseases. In this study, we measured various conformational toxic species of Aβ and markers of inflammation, apoptosis, endolysosomal degradation, and neuroprotection after 5 months of exercise training (ET), resveratrol (Resv) treatment, or combination treatment in the 3xTg-AD mouse model of AD. Our main results indicate that Resv decreased neuroinflammation and accumulation of Aβ oligomers, increased levels of neurotrophins, synaptic markers, silent information regulator, and decreased markers of apoptosis, autophagy, endolysosomal degradation and ubiquitination in the brains of 3xTg-AD mice. ET improved some markers related to neuroprotection, but when combined with Resv treatment, the benefits achieved were as effective as Resv treatment alone. Our results show that the neuroprotective effects of Resv, ET or Resv and ET are associated with reduced toxicity of Aβ oligomers, suppression of neuronal autophagy, decreased apoptosis, and upregulation of key growth-related proteins.
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Affiliation(s)
- Tom L. Broderick
- Department of Physiology, College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA;
- Laboratory of Diabetes and Exercise Metabolism, College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA;
- Correspondence: (T.L.B.); (J.R.B.)
| | - Suhail Rasool
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA; (S.R.); (R.L.); (Y.Z.); (T.G.)
| | - Rongzi Li
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA; (S.R.); (R.L.); (Y.Z.); (T.G.)
| | - Yuxian Zhang
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA; (S.R.); (R.L.); (Y.Z.); (T.G.)
| | - Miranda Anderson
- Laboratory of Diabetes and Exercise Metabolism, College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA;
| | - Layla Al-Nakkash
- Department of Physiology, College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA;
| | - Jeffrey H. Plochocki
- Department of Medical Education, University of Central Florida, College of Medicine, 6850 Lake Nona Blvd, Orlando, FL 32827, USA;
| | - Thangiah Geetha
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA; (S.R.); (R.L.); (Y.Z.); (T.G.)
| | - Jeganathan Ramesh Babu
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL 36849, USA; (S.R.); (R.L.); (Y.Z.); (T.G.)
- Correspondence: (T.L.B.); (J.R.B.)
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2
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Levine ZA, Teranishi K, Okada AK, Langen R, Shea JE. The Mitochondrial Peptide Humanin Targets but Does Not Denature Amyloid Oligomers in Type II Diabetes. J Am Chem Soc 2019; 141:14168-14179. [DOI: 10.1021/jacs.9b04995] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, United States
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3
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Ghosh S, T D, Baul U, Vemparala S. Aggregation dynamics of charged peptides in water: Effect of salt concentration. J Chem Phys 2019; 151:074901. [DOI: 10.1063/1.5100890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Susmita Ghosh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Devanand T
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Upayan Baul
- Institue of Physics, Albert-Ludwigs-University of Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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4
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Matthes D, Gapsys V, Brennecke JT, de Groot BL. An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase. Sci Rep 2016; 6:33156. [PMID: 27616019 PMCID: PMC5018807 DOI: 10.1038/srep33156] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023] Open
Abstract
The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils.
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Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julian T Brennecke
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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5
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Kumar S, Birol M, Schlamadinger DE, Wojcik SP, Rhoades E, Miranker AD. Foldamer-mediated manipulation of a pre-amyloid toxin. Nat Commun 2016; 7:11412. [PMID: 27108700 PMCID: PMC4848510 DOI: 10.1038/ncomms11412] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/22/2016] [Indexed: 01/15/2023] Open
Abstract
Disordered proteins, such as those central to Alzheimer's and Parkinson's, are particularly intractable for structure-targeted therapeutic design. Here we demonstrate the capacity of a synthetic foldamer to capture structure in a disease relevant peptide. Oligoquinoline amides have a defined fold with a solvent-excluded core that is independent of its outwardly projected, derivatizable moieties. Islet amyloid polypeptide (IAPP) is a peptide central to β-cell pathology in type II diabetes. A tetraquinoline is presented that stabilizes a pre-amyloid, α-helical conformation of IAPP. This charged, dianionic compound is readily soluble in aqueous buffer, yet crosses biological membranes without cellular assistance: an unexpected capability that is a consequence of its ability to reversibly fold. The tetraquinoline docks specifically with intracellular IAPP and rescues β-cells from toxicity. Taken together, our work here supports the thesis that stabilizing non-toxic conformers of a plastic protein is a viable strategy for cytotoxic rescue addressable using oligoquinoline amides.
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Affiliation(s)
- Sunil Kumar
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Melissa Birol
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Diana E. Schlamadinger
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Slawomir P. Wojcik
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Elizabeth Rhoades
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
| | - Andrew D. Miranker
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
- Department of Chemical and Environmental Engineering, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
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6
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Nagel-Steger L, Owen MC, Strodel B. An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations. Chembiochem 2016; 17:657-76. [PMID: 26910367 DOI: 10.1002/cbic.201500623] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 12/27/2022]
Abstract
The deposition of amyloid in brain tissue in the context of neurodegenerative diseases involves the formation of intermediate species-termed oligomers-of lower molecular mass and with structures that deviate from those of mature amyloid fibrils. Because these oligomers are thought to be primarily responsible for the subsequent disease pathogenesis, the elucidation of their structure is of enormous interest. Nevertheless, because of the high aggregation propensity and the polydispersity of oligomeric species formed by the proteins or peptides in question, the preparation of appropriate samples for high-resolution structural methods has proven to be rather difficult. This is why theoretical approaches have been of particular importance in gaining insights into possible oligomeric structures for some time. Only recently has it been possible to achieve some progress with regard to the experimentally based structural characterization of defined oligomeric species. Here we discuss how theory and experiment are used to determine oligomer structures and what can be done to improve the integration of the two disciplines.
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Affiliation(s)
- Luitgard Nagel-Steger
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany
| | - Michael C Owen
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany.
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7
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Guerrero-Muñoz MJ, Gerson J, Castillo-Carranza DL. Tau Oligomers: The Toxic Player at Synapses in Alzheimer's Disease. Front Cell Neurosci 2015; 9:464. [PMID: 26696824 PMCID: PMC4667007 DOI: 10.3389/fncel.2015.00464] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 11/16/2015] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive disorder in which the most noticeable symptoms are cognitive impairment and memory loss. However, the precise mechanism by which those symptoms develop remains unknown. Of note, neuronal loss occurs at sites where synaptic dysfunction is observed earlier, suggesting that altered synaptic connections precede neuronal loss. The abnormal accumulation of amyloid-β (Aβ) and tau protein is the main histopathological feature of the disease. Several lines of evidence suggest that the small oligomeric forms of Aβ and tau may act synergistically to promote synaptic dysfunction in AD. Remarkably, tau pathology correlates better with the progression of the disease than Aβ. Recently, a growing number of studies have begun to suggest that missorting of tau protein from the axon to the dendrites is required to mediate the detrimental effects of Aβ. In this review we discuss the novel findings regarding the potential mechanisms by which tau oligomers contribute to synaptic dysfunction in AD.
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Affiliation(s)
- Marcos J Guerrero-Muñoz
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston TX, USA ; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Julia Gerson
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston TX, USA ; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Diana L Castillo-Carranza
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston TX, USA ; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston TX, USA
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8
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White EM, Miranker AD. A solenoid design for assessing determinants of parallel β-sheet registration. Protein Eng Des Sel 2015; 28:577-83. [PMID: 26487712 DOI: 10.1093/protein/gzv053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 09/17/2015] [Indexed: 11/12/2022] Open
Abstract
A novel protein construct is presented that combines a homotrimeric, triple-stranded β-helix as a guest to a homotrimeric foldon unit from bacteriophage T4 fibritin. The β-helical solenoid selected is short (46 residues) and is part of a subdomain of the T4 cell-puncturing device. The resultant design is trimeric and displays greatly enhanced stability over each sub-component alone. The intended goal is a design that will enable evaluation of sequence determinants that promote in-register versus out-of-register parallel β-sheet homotrimerization. Towards that end, the importance of a set of three buried salt-bridges was evaluated by converting them to residues otherwise consistently found throughout the natural solenoid at the same positions. The critical role of the charged residues in the salt-bridges was evident in that their elimination resulted in amyloid-like aggregation.
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Affiliation(s)
- Ellen M White
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA
| | - Andrew D Miranker
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA
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9
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Abstract
![]()
Homomeric self-assembly of peptides
into amyloid fibers is a feature of many diseases. A central role
has been suggested for the lateral fiber surface affecting gains of
toxic function. To investigate this, a protein scaffold that presents
a discrete, parallel β-sheet surface for amyloid subdomains
up to eight residues in length has been designed. Scaffolds that present
the fiber surface of islet amyloid polypeptide (IAPP) were prepared.
The designs show sequence-specific surface effects apparent in that
they gain the capacity to attenuate rates of IAPP self-assembly in
solution and affect IAPP-induced toxicity in insulin-secreting cells.
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Affiliation(s)
- Marisa A Rubio
- Department of Molecular Biophysics and Biochemistry, Yale University , 260 Whitney Avenue, New Haven, Connecticut 06520-8114, United States
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10
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Gerson JE, Castillo-Carranza DL, Kayed R. Advances in therapeutics for neurodegenerative tauopathies: moving toward the specific targeting of the most toxic tau species. ACS Chem Neurosci 2014; 5:752-69. [PMID: 25075869 DOI: 10.1021/cn500143n] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative disease is one of the greatest health concerns today and with no effective treatment in sight, it is crucial that researchers find a safe and successful therapeutic. While neurofibrillary tangles are considered the primary tauopathy hallmark, more evidence continues to come to light to suggest that soluble, intermediate tau aggregates--tau oligomers--are the most toxic species in disease. These intermediate tau species may also be responsible for the spread of pathology, suggesting that oligomeric tau may be the best therapeutic target. Here, we summarize results for the modulation of tau by molecular chaperones, small molecules and aggregation inhibitors, post-translational modifications, immunotherapy, other techniques, and future directions.
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Affiliation(s)
- Julia E. Gerson
- Department
of Neurology, George and Cynthia Mitchell
Center for Alzheimer’s Disease Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Diana L. Castillo-Carranza
- Department
of Neurology, George and Cynthia Mitchell
Center for Alzheimer’s Disease Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Rakez Kayed
- Department
of Neurology, George and Cynthia Mitchell
Center for Alzheimer’s Disease Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
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11
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Kumar S, Brown MA, Nath A, Miranker AD. Folded small molecule manipulation of islet amyloid polypeptide. ACTA ACUST UNITED AC 2014; 21:775-81. [PMID: 24930968 DOI: 10.1016/j.chembiol.2014.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 11/27/2022]
Abstract
Islet amyloid polypeptide (IAPP) is a hormone cosecreted with insulin by pancreatic β cells. Upon contact with lipid bilayers, it is stabilized into a heterogeneous ensemble of structural states. These processes are associated with gains of function, including catalysis of β sheet-rich amyloid formation, cell membrane penetration, loss of membrane integrity, and cytotoxicity. These contribute to the dysfunction of β cells, a central component in the pathology and treatment of diabetes. To gain mechanistic insight into these phenomena, a related series of substituted oligoquinolines were designed. These inhibitors are unique in that they have the capacity to affect both solution- and phospholipid bilayer-catalyzed IAPP self-assembly. Importantly, we show that this activity is associated with the oligoquinoline's capacity to irreversibly adopt a noncovalent fold. This suggests that compact foldamer scaffolds, such as oligoquinoline, are an important paradigm for conformational manipulation of disordered protein state.
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Affiliation(s)
- Sunil Kumar
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA
| | - Mark A Brown
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA
| | - Abhinav Nath
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA
| | - Andrew D Miranker
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA.
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12
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Gerson JE, Kayed R. Formation and propagation of tau oligomeric seeds. Front Neurol 2013; 4:93. [PMID: 23882255 PMCID: PMC3713404 DOI: 10.3389/fneur.2013.00093] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 07/01/2013] [Indexed: 12/14/2022] Open
Abstract
Tau misfolding and aggregation leads to the formation of neurofibrillary tangles (NFTs), which have long been considered one of the main pathological hallmarks for numerous neurodegenerative diseases known as tauopathies, including Alzheimer’s Disease (AD) and Parkinson’s Disease (PD). However, recent studies completed both in vitro and in vivo suggest that intermediate forms of tau, known as tau oligomers, between the monomeric form and NFTs are the true toxic species in disease and the best targets for anti-tau therapies. However, the exact mechanism by which the spread of pathology occurs is unknown. Evidence suggests that tau oligomers may act as templates for the misfolding of native tau, thereby seeding the spread of the toxic forms of the protein. Recently, researchers have reported the ability of tau oligomers to enter and exit cells, propagating from disease-affected regions to unaffected areas. While the mechanism by which the spreading of misfolded tau occurs has yet to be elucidated, there are a few different models which have been proposed, including cell membrane stress and pore-formation, endocytosis and exocytosis, and non-traditional secretion of protein not enclosed by a membrane. Coming to an understanding of how toxic tau species seed and spread through the brain will be crucial to finding effective treatments for neurodegenerative tauopathies.
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Affiliation(s)
- Julia E Gerson
- George P. and Cynthia Woods Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch , Galveston, TX , USA ; Department of Neurology, University of Texas Medical Branch , Galveston, TX , USA ; Department of Neuroscience and Cell Biology, University of Texas Medical Branch , Galveston, TX , USA
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13
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Esue O, Xie AX, Kamerzell TJ, Patapoff TW. Thermodynamic and structural characterization of an antibody gel. MAbs 2013; 5:323-34. [PMID: 23425660 DOI: 10.4161/mabs.23183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although extensively studied, protein-protein interactions remain highly elusive and are of increasing interest in drug development. We show the assembly of a monoclonal antibody, using multivalent carboxylate ions, into highly-ordered structures. While the presence and function of similar structures in vivo are not known, the results may present a possible unexplored area of antibody structure-function relationships. Using a variety of tools (e.g., mechanical rheology, electron microscopy, isothermal calorimetry, Fourier transform infrared spectroscopy), we characterized the physical, biochemical, and thermodynamic properties of these structures and found that citrate may interact directly with the amino acid residue histidine, after which the individual protein units assemble into a filamentous network gel exhibiting high elasticity and interfilament interactions. Citrate interacts exothermically with the monoclonal antibody with an association constant that is highly dependent on solution pH and temperature. Secondary structure analysis also reveals involvement of hydrophobic and aromatic residues.
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Affiliation(s)
- Osigwe Esue
- Pharmaceutical Development, Genentech, South San Francisco, CA, USA.
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14
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Casasnovas R, Ortega-Castro J, Donoso J, Frau J, Muñoz F. Theoretical calculations of stability constants and pKa values of metal complexes in solution: application to pyridoxamine–copper(ii) complexes and their biological implications in AGE inhibition. Phys Chem Chem Phys 2013; 15:16303-13. [DOI: 10.1039/c3cp50840d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Ma B, Nussinov R. Selective molecular recognition in amyloid growth and transmission and cross-species barriers. J Mol Biol 2012; 421:172-84. [PMID: 22119878 PMCID: PMC6407624 DOI: 10.1016/j.jmb.2011.11.023] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/10/2011] [Accepted: 11/13/2011] [Indexed: 11/23/2022]
Abstract
Mutual conformational selection and population shift followed by minor induced-fit optimization is the key mechanism in biomolecular recognition, and monomers and small oligomers binding to amyloid seeds in fibril growth is a molecular recognition event. Here, we describe amyloid aggregation, preferred species, cross-species barriers and transmission within the broad framework of molecular recognition. Cross-seeding of amyloid species is governed by conformational selection of compatible (complementary) states. If the dominant conformations of two species are similar, they can cross-seed each other; on the other hand, if they are sufficiently different, they will grow into different fibrils, reflecting species barriers. Such a scenario has recently been observed for the tau protein, which has four repeats. While a construct consisting of repeats 1, 3 and 4 can serve as a seed for the entire four-repeat tau segment, the inverse does not hold. On the other hand, the tau protein repeats with the characteristic U-turn shape can cross-seed Alzheimer's amyloid β and, similarly, the islet amyloid polypeptide. Within this framework, we suggest that the so-called "central dogma" of amyloid formation, where aggregation takes place through nonspecific backbone hydrogen bonding interactions, which are common to all peptides and proteins, is a simple reflection of the heterogeneous, polymorphic free-energy landscape of amyloid species. Here, we review available data and make some propositions addressing this key problem. In particular, we argue that recent theoretical and experimental observations support the key role of selective molecular recognition in amyloidosis and in determining cross-species barriers and transmission.
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Affiliation(s)
- Buyong Ma
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program NCI-Frederick, Frederick, MD 21702
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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16
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Matthes D, Gapsys V, de Groot BL. Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations. J Mol Biol 2012; 421:390-416. [PMID: 22326493 DOI: 10.1016/j.jmb.2012.02.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 01/27/2012] [Accepted: 02/01/2012] [Indexed: 12/20/2022]
Abstract
Understanding the structural and energetic requirements of non-fibrillar oligomer formation harbors the potential to decipher an important yet still elusive part of amyloidogenic peptide and protein aggregation. Low-molecular-weight oligomers are described to be transient and polymorphic intermediates in the nucleated self-assembly process to highly ordered amyloid fibers and were additionally found to exhibit a profound cytotoxicity. However, detailed structural information on the oligomeric species involved in the nucleation cannot be readily inferred from experiments. Here, we study the spontaneous assembly of steric zipper peptides from the tau protein, insulin and α-synuclein with atomistic molecular dynamics simulations on the microsecond timescale. Detailed analysis of the forces driving the oligomerization reveals a common two-step process akin to a general condensation-ordering mechanism and thus provides a rational understanding of the molecular basis of peptide self-assembly. Our results suggest that the initial formation of partially ordered peptide oligomers is governed by the solvation free energy, whereas the dynamical ordering and emergence of β-sheets are mainly driven by optimized inter-peptide interactions in the collapsed state. A novel mapping technique based on collective coordinates is employed to highlight similarities and differences in the conformational ensemble of small oligomer structures. Elucidating the dynamical and polymorphic β-sheet oligomer conformations at atomistic detail furthermore suggests complementary sheet packing characteristics similar to steric zipper structures, but with a larger heterogeneity in the strand alignment pattern and sheet-to-sheet arrangements compared to the cross-β motif found in the fibrillar or crystalline states.
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Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry Am Fassberg 11, 37077 Göttingen, Germany
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Schuster TB, Ouboter DDB, Palivan CG, Meier W. From fibers to micelles using point-mutated amphiphilic peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:4578-4584. [PMID: 21413731 DOI: 10.1021/la200443p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Biocompatible, self-assembled nanostructures are attracting ever more attention, in particular in aqueous media for biomedical applications. Here, we present the successful, solid-phase peptide synthesis (SPPS) and characterization of short amino acid sequences with amphiphilic character with the aim of gaining insight into their self-assembled, supramolecular structures. The peptide design includes three parts: (a) a charged lysine part, (b) an acetylated lysine part, and (c) a constant hydrophobic rodlike helix, based on gramicidin A (gA). By stepwise replacement of free lysine (K) with acetylated lysine (X) we generated a library of a total of 10 peptides, Ac-X(8)-gA and K(m)X(8-m)-gA (m ranging from 0 to 8). By using point mutations, we adjusted the degree of acetylation (DA) and thus the overall amphiphilicity of the peptides, which led to a change in the secondary structure in the aqueous environment from a β-sheet to an α-helix. This transition generated a significant change in the morphology of the self-assembled structures from fibers to micelles. Two different regions were observed for the conformation of the hydrophilic part of the peptide: one region, a β-sheet-like secondary structure, inducing fiber formation (high DA), the other an α-helical-like secondary structure, generating micelle formation (moderate and low DA). The micellar structures depended on the degree of acetylation, which influenced their critical micelle concentration (cmc). These morphology regions were determined by a combination of circular dichroism, dynamic light scattering, surface tension, and transmission electron microscopy, which allowed us to correlate the generated supramolecular architectures with the fine changes obtained by means of the point mutation strategy.
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Affiliation(s)
- Thomas B Schuster
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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