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Cieplak AS. Tau Inclusions in Alzheimer's, Chronic Traumatic Encephalopathy and Pick's Disease. A Speculation on How Differences in Backbone Polarization Underlie Divergent Pathways of Tau Aggregation. Front Neurosci 2019; 13:488. [PMID: 31156372 PMCID: PMC6530265 DOI: 10.3389/fnins.2019.00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022] Open
Abstract
Tau-related dementias appear to involve specific to each disease aggregation pathways and morphologies of filamentous tau assemblies. To understand etiology of these differences, here we elucidate molecular mechanism of formation of tau PHFs based on the PMO theory of misfolding and aggregation of pleiomorphic proteins associated with neurodegenerative diseases. In this model, fibrillization of tau is initiated by the coupled binding and folding of the MTB domains that yields antiparallel homodimers, in analogy to folding of split inteins. The free energy of binding is minimized when the antiparallel alignment brings about backbone-backbone H-bonding between the MTBD segments of similar "strand" propensities. To assess these propensities, a function of the NMR shielding tensors of the Cα atoms is introduced as the folding potential function FP i ; the Cα tensors are obtained by the quantum mechanical modeling of protein secondary structure (GIAO//B3LYP/D95**). The calculated FP i plots show that the "strand" propensities of the MBTD segments, and hence the homodimer's register, can be affected by the relatively small changes in the environment's pH, as a result of protonation of MBTD's conserved histidines. The assembly of the antiparallel tau dimers into granular aggregates and their subsequent conversion into the parallel cross-β structure of paired helical filaments is expected to follow the same path as the previously described fibrillization of Aβ. Consequently, the core structure of the nascent tau fibril is determined by the register of the tau homodimer. This model accounts for the reported differences in (i) fibril-core structure of in vivo and in vitro filaments, (ii) cross-seeding of isoforms, (iii) effects of reducing/non-reducing conditions, (iv) effects of PHF6 mutations, and (v) homologs' aggregation properties. The proposed model also suggests that in contrast to Alzheimer's and chronic traumatic encephalopathy disease, the assembly of tau prions in Pick's disease would be facilitated by a moderate drop in pH that accompanies e.g., transit in the endosomal system, inflammation response or an ischemic injury.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Brandeis University, Waltham, MA, United States
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2
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Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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Lee J, Jang G, Kang P, Choi MG, Choi SH. Helical α/β-depsipeptides with alternating residue types: conformational change from the 11-helix to the 14/15-helix. Org Biomol Chem 2016; 14:8438-42. [DOI: 10.1039/c6ob01602b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Short α/β-depsipeptides of which the third residue from the N-terminus is an (S)-lactic acid residue predominantly adopt 14/15-helical conformations analogous to the α-helix.
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Affiliation(s)
- Jaeyeon Lee
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
| | - Geunhyeok Jang
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
| | - Philjae Kang
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
| | - Moon-Gun Choi
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
| | - Soo Hyuk Choi
- Department of Chemistry
- Yonsei University
- Seoul
- Republic of Korea
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Thirupathi R, Prabhakaran EN. Estimation of the 2.05 helix type i→i hydrogen bond energy at Aib∗-Oxa motif: an isodesmic approach. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.04.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
Peptide-bond isosteres can enable a deep interrogation of the structure and function of a peptide or protein by amplifying or attenuating particular chemical properties. In this Minireview, the electronic, structural, and conformational attributes of four such isosteres-thioamides, esters, alkenes, and fluoroalkenes-are examined in detail. In particular, the ability of these isosteres to partake in noncovalent interactions is compared with that of the peptide bond. The consequential perturbations provide a useful tool for chemical biologists to reveal new structure-function relationships, and to endow peptides and proteins with desirable attributes.
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Affiliation(s)
- Amit Choudhary
- Graduate Program in Biophysics, University of Wisconsin–Madison, 1525 Linden Drive, Madison, WI 53706-1534 (USA)
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544 (USA), Fax: (+1) 608-890-2583
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Avenue, Madison, WI 53706-1322 (USA)
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Avan I, Tala SR, Steel PJ, Katritzky AR. Benzotriazole-Mediated Syntheses of Depsipeptides and Oligoesters. J Org Chem 2011; 76:4884-93. [DOI: 10.1021/jo200174j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ilker Avan
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Department of Chemistry, Anadolu University, 26470, Eskişehir, Turkey
| | - Srinivasa R. Tala
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Peter J. Steel
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand
| | - Alan R. Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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Kang YK, Byun BJ. Conformational Preferences and Cis−Trans Isomerization of l-Lactic Acid Residue. J Phys Chem B 2008; 112:9126-34. [DOI: 10.1021/jp801200m] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Byung Jin Byun
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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Oku H, Yamada K, Katakai R. Conformational change from antiparallel beta-sheet to alpha-helix in a series of depsipeptide, -(Leu-Leu-Lac)(n)-: syntheses, spectroscopic studies, and crystal structures of Boc-Leu-Lac-OEt and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2). Biopolymers 2008; 89:270-83. [PMID: 18067154 DOI: 10.1002/bip.20904] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The depsipeptides Boc-Leu-Lac-OEt (1) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 1, 2) (2 and 3, respectively) (Boc = tert-butyloxycarbonyl, Lac = L-lactic acid residue) has been synthesized and studied by crystallographic, CD spectroscopic, and ESI-MS analyses. In the packing cells, those three compounds adopt beta-strand conformations. Each molecule is linked into a dimer (1) or an infinite assembly (2 and 3) by tight hydrogen bonds of the type NH...O==C. Interestingly, the hexamer, 3 shows the first example of antiparallel pleated beta-sheet crystal structure for a depsipeptide molecule. In the packing cells, especially for 3, the ester groups O--C==O are perpendicularly oriented to the amide groups NH--C==O and beta-sheet planes to avoid the interaction between --O--(ester) and O==C. Therefore, when the chain length become longer, the O...O==C repulsion interaction works as a beta-sheet breaker and hence promotes an alpha-helical structure as observed for Boc-(Leu-Leu-Lac)(3)-Leu-Leu-OEt (4) (Oku et al. Biopolymers 2004, 75, 242-254) and Boc-(Leu-Leu-Lac)(n)-OEt (n = 4-6) (5-7) (Katakai et al., Biopolymers 1996, 38, 285-290), in which the O...O==C repulsion does not cause significant structural changes in alpha-helical main chains. Therefore from the structural and spectroscopic analyses, we have found governing factors for the specificity in the beta-sheet and alpha-helix decision in this series of depsipeptides, -(Leu-Leu-Lac)(n)-.
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Affiliation(s)
- Hiroyuki Oku
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Gunma, Japan.
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Gao J, Kelly JW. Toward quantification of protein backbone-backbone hydrogen bonding energies: An energetic analysis of an amide-to-ester mutation in an alpha-helix within a protein. Protein Sci 2008; 17:1096-101. [PMID: 18434500 DOI: 10.1110/ps.083439708] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Amide-to-ester backbone mutagenesis enables a specific backbone-backbone hydrogen bond (H-bond) in a protein to be eliminated in order to quantify its energetic contribution to protein folding. To extract a H-bonding free energy from an amide-to-ester perturbation free energy (DeltaG (folding,wt) - DeltaG (folding,mut)), it is necessary to correct for the putative introduction of a lone pair-lone pair electrostatic repulsion, as well as for the transfer free energy differences that may arise between the all amide sequence and the predominantly amide sequence harboring an ester bond. Mutation of the 9-10 amide bond within the V9F variant of the predominantly helical villin headpiece subdomain (HP35) to an ester or an E-olefin backbone bond results in a less stable but defined wild-type fold, an attribute required for this study. Comparing the folding free energies of the ester and E-olefin mutants, with correction for the desolvation free energy differences (ester and E-olefin) and the loss of an n-to-pi* interaction (E-olefin), yields an experimentally based estimate of +0.4 kcal/mol for the O-O repulsion energy in an alpha-helical context, analogous to our previous experimentally based estimate of the O-O repulsion free energy in the context of a beta-sheet. The small O-O repulsion energy indicates that amide-to-ester perturbation free energies can largely be attributed to the deletion of the backbone H-bonds after correction for desolvation differences. Quantitative evaluation of H-bonding in an alpha-helix should now be possible, an important step toward deciphering the balance of forces that enable spontaneous protein folding.
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Affiliation(s)
- Jianmin Gao
- Department of Chemistry and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Scheike JA, Baldauf C, Spengler J, Albericio F, Pisabarro MT, Koksch B. Amide-to-Ester Substitution in Coiled Coils: The Effect of Removing Hydrogen Bonds on Protein Structure. Angew Chem Int Ed Engl 2007; 46:7766-9. [PMID: 17876795 DOI: 10.1002/anie.200702218] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jessica A Scheike
- Department of Chemistry and Biochemistry, Free University of Berlin, Takustrasse 3, 14195 Berlin, Germany
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Scheike J, Baldauf C, Spengler J, Albericio F, Pisabarro M, Koksch B. Estersubstitutionen in α-helicalen Coiled-Coil-Peptiden: Effekt der Eliminierung von Wasserstoffbrücken auf die Struktur von Proteinen. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200702218] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Wieczorek R, Dannenberg JJ. The Energetic and Structural Effects of Single Amino Acid Substitutions upon Capped α-Helical Peptides Containing 17 Amino Acid Residues. An ONIOM DFT/AM1 Study. J Am Chem Soc 2005; 127:17216-23. [PMID: 16332068 DOI: 10.1021/ja052689j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We evaluate the effect of the amino acid mutations of glycine, leucine, valine, phenylalanine, serine, and proline for the 10th alanine in the capped peptide, acetly(Ala)(17)NH(2), upon the energies of the alpha-helices and beta-strands using ONIOM DFT/AM1 molecular orbital calculations. The relative stabilities of the alpha-helix (to the beta-strand) derive from the differences between the effects upon not only the helix but the strand as well. Thus, Ala --> Pro significantly destabilizes both but destabilizes the alpha-helix more, while Ala --> Gly stabilizes both but stabilizes the beta-strand more. The theoretical results are discussed in the context of the known experimental reports. We suggest that the solvation of the unfolded state drives the helix/coil equilibrium in solution.
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Affiliation(s)
- Robert Wieczorek
- Department of Chemistry, City University of New York, Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10021, USA
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Powers ET, Deechongkit S, Kelly JW. Backbone-Backbone H-Bonds Make Context-Dependent Contributions to Protein Folding Kinetics and Thermodynamics: Lessons from Amide-to-Ester Mutations. ADVANCES IN PROTEIN CHEMISTRY 2005; 72:39-78. [PMID: 16581372 DOI: 10.1016/s0065-3233(05)72002-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The contribution of backbone-backbone hydrogen bonds (H-bonds) to protein folding energetics has been controversial. This is due, at least in part, to the inability to perturb backbone-backbone H-bonds by traditional methods of protein mutagenesis. Recently, however, protein backbone mutagenesis has become possible with the development of chemical and biological methods to replace individual amides in the protein backbone with esters. Here, we review the use of amide-to-ester mutation as a tool to evaluate the contribution of backbone-backbone H-bonds to protein folding kinetics and thermodynamics.
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Affiliation(s)
- Evan T Powers
- Department of Chemistry and The Skaggs Institute for Chemical Biology The Scripps Research Institute, La Jolla, California 92037
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