1
|
Moldovean-Cioroianu NS. Reviewing the Structure-Function Paradigm in Polyglutamine Disorders: A Synergistic Perspective on Theoretical and Experimental Approaches. Int J Mol Sci 2024; 25:6789. [PMID: 38928495 PMCID: PMC11204371 DOI: 10.3390/ijms25126789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Polyglutamine (polyQ) disorders are a group of neurodegenerative diseases characterized by the excessive expansion of CAG (cytosine, adenine, guanine) repeats within host proteins. The quest to unravel the complex diseases mechanism has led researchers to adopt both theoretical and experimental methods, each offering unique insights into the underlying pathogenesis. This review emphasizes the significance of combining multiple approaches in the study of polyQ disorders, focusing on the structure-function correlations and the relevance of polyQ-related protein dynamics in neurodegeneration. By integrating computational/theoretical predictions with experimental observations, one can establish robust structure-function correlations, aiding in the identification of key molecular targets for therapeutic interventions. PolyQ proteins' dynamics, influenced by their length and interactions with other molecular partners, play a pivotal role in the polyQ-related pathogenic cascade. Moreover, conformational dynamics of polyQ proteins can trigger aggregation, leading to toxic assembles that hinder proper cellular homeostasis. Understanding these intricacies offers new avenues for therapeutic strategies by fine-tuning polyQ kinetics, in order to prevent and control disease progression. Last but not least, this review highlights the importance of integrating multidisciplinary efforts to advancing research in this field, bringing us closer to the ultimate goal of finding effective treatments against polyQ disorders.
Collapse
Affiliation(s)
- Nastasia Sanda Moldovean-Cioroianu
- Institute of Materials Science, Bioinspired Materials and Biosensor Technologies, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany;
- Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, RO-400084 Cluj-Napoca, Romania
| |
Collapse
|
2
|
Harper M, Nudurupati U, Workman RJ, Lakoba TI, Perez N, Nelson D, Ou Y, Punihaole D. Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy. J Chem Phys 2023; 159:225101. [PMID: 38078532 PMCID: PMC10720587 DOI: 10.1063/5.0177437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
We present structural models for three different amyloid fibril polymorphs prepared from amylin20-29 (sequence SNNFGAILSS) and amyloid-β25-35 (Aβ25-35) (sequence GSNKGAIIGLM) peptides. These models are based on the amide C=O bond and Ramachandran ψ-dihedral angle data from Raman spectroscopy, which were used as structural constraints to guide molecular dynamics (MD) simulations. The resulting structural models indicate that the basic structural motif of amylin20-29 and Aβ25-35 fibrils is extended β-strands. Our data indicate that amylin20-29 forms both antiparallel and parallel β-sheet fibril polymorphs, while Aβ25-35 forms a parallel β-sheet fibril structure. Overall, our work lays the foundation for using Raman spectroscopy in conjunction with MD simulations to determine detailed molecular-level structural models of amyloid fibrils in a manner that complements gold-standard techniques, such as solid-state nuclear magnetic resonance and cryogenic electron microscopy.
Collapse
Affiliation(s)
- Madeline Harper
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Uma Nudurupati
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Riley J. Workman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Taras I. Lakoba
- Department of Mathematics and Statistics, University of Vermont, Burlington, Vermont 05405, USA
| | - Nicholas Perez
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Delaney Nelson
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Yangguang Ou
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - David Punihaole
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| |
Collapse
|
3
|
Kandola T, Venkatesan S, Zhang J, Lerbakken BT, Von Schulze A, Blanck JF, Wu J, Unruh JR, Berry P, Lange JJ, Box AC, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. eLife 2023; 12:RP86939. [PMID: 37921648 PMCID: PMC10624427 DOI: 10.7554/elife.86939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
Collapse
Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical ResearchKansas CityUnited States
- The Open UniversityMilton KeynesUnited Kingdom
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | | | | | | | - Jianzheng Wu
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical CenterKansas CityUnited States
| | - Jay R Unruh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Paula Berry
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Andrew C Box
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Malcolm Cook
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Celeste Sagui
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | - Randal Halfmann
- Stowers Institute for Medical ResearchKansas CityUnited States
| |
Collapse
|
4
|
Kandola T, Venkatesan S, Zhang J, Lerbakken B, Schulze AV, Blanck JF, Wu J, Unruh J, Berry P, Lange JJ, Box A, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533418. [PMID: 36993401 PMCID: PMC10055281 DOI: 10.1101/2023.03.20.533418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
Collapse
Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The Open University, Milton Keyes, MK7 6AA, UK
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Alex Von Schulze
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jillian F Blanck
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jianzheng Wu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paula Berry
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Malcolm Cook
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| |
Collapse
|
5
|
Mustafa R, Fitian M, Hamilton NB, Li J, Silva WR, Punihaole D. Molecular Insights into the Binding of Linear Polyethylenimines and Single-Stranded DNA Using Raman Spectroscopy: A Quantitative Approach. J Phys Chem B 2022; 126:8404-8414. [PMID: 36222425 PMCID: PMC10413332 DOI: 10.1021/acs.jpcb.2c04939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Establishing how polymeric vectors such as polyethylenimine (PEI) bind and package their nucleic acid cargo is vital toward developing more efficacious and cost-effective gene therapies. To develop a molecular-level picture of DNA binding, we examined how the Raman spectra of PEIs report on their local chemical environment. We find that the intense Raman bands located in the 1400-1500 cm-1 region derive from vibrations with significant CH2 scissoring and NH bending character. The Raman bands that derive from these vibrations show profound intensity changes that depend on both the local dielectric environment and hydrogen bonding interactions with the secondary amine groups on the polymer. We use these bands as spectroscopic markers to assess the binding between low molecular weight PEIs and single-stranded DNA (ssDNA). Analysis of the Raman spectra suggest that PEI primarily binds via electrostatic interactions to the phosphate backbone, which induces the condensation of the ssDNA. We additionally confirm this finding by conducting molecular dynamics simulations. We expect that the spectral correlations determined here will enable future studies to investigate important gene delivery activities, including how PEI interacts with cellular membranes to facilitate cargo internalization into cells.
Collapse
Affiliation(s)
- Rusul Mustafa
- Department of Chemistry, University of Vermont, Burlington, Vermont05405, United States
| | - Maria Fitian
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York12211, United States
| | - Nicholas B Hamilton
- Department of Chemistry, University of Vermont, Burlington, Vermont05405, United States
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, Vermont05405, United States
| | - W Ruchira Silva
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York12211, United States
| | - David Punihaole
- Department of Chemistry, University of Vermont, Burlington, Vermont05405, United States
| |
Collapse
|
6
|
Van Bruggen C, Punihaole D, Keith AR, Schmitz AJ, Tolar J, Frontiera RR, Reineke TM. Quinine copolymer reporters promote efficient intracellular DNA delivery and illuminate a protein-induced unpackaging mechanism. Proc Natl Acad Sci U S A 2020; 117:32919-32928. [PMID: 33318196 PMCID: PMC7777095 DOI: 10.1073/pnas.2016860117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Polymeric vehicles that efficiently package and controllably release nucleic acids enable the development of safer and more efficacious strategies in genetic and polynucleotide therapies. Developing delivery platforms that endogenously monitor the molecular interactions, which facilitate binding and release of nucleic acids in cells, would aid in the rational design of more effective vectors for clinical applications. Here, we report the facile synthesis of a copolymer containing quinine and 2-hydroxyethyl acrylate that effectively compacts plasmid DNA (pDNA) through electrostatic binding and intercalation. This polymer system poly(quinine-co-HEA) packages pDNA and shows exceptional cellular internalization, transgene expression, and low cytotoxicity compared to commercial controls for several human cell lines, including HeLa, HEK 293T, K562, and keratinocytes (N/TERTs). Using quinine as an endogenous reporter for pDNA intercalation, Raman imaging revealed that proteins inside cells facilitate the unpackaging of polymer-DNA complexes (polyplexes) and the release of their cargo. Our work showcases the ability of this quinine copolymer reporter to not only facilitate effective gene delivery but also enable diagnostic monitoring of polymer-pDNA binding interactions on the molecular scale via Raman imaging. The use of Raman chemical imaging in the field of gene delivery yields unprecedented insight into the unpackaging behavior of polyplexes in cells and provides a methodology to assess and design more efficient delivery vehicles for gene-based therapies.
Collapse
Affiliation(s)
- Craig Van Bruggen
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - David Punihaole
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - Allison R Keith
- Department of Pediatrics, Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Andrew J Schmitz
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - Jakub Tolar
- Department of Pediatrics, Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455;
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455;
| |
Collapse
|
7
|
Paul S, Kumari K, Paul S. Molecular Insight into the Effects of Enhanced Hydrophobicity on Amyloid-like Aggregation. J Phys Chem B 2020; 124:10048-10061. [PMID: 33115237 DOI: 10.1021/acs.jpcb.0c06000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Generally, hydrophobic amino acids provide hydrophobic interactions during peptide aggregation. However, besides the hydrophobic amino acids, some hydrophilic amino acids, such as glutamine, are also considered to be essential elements in many self-aggregating peptides. For example, huntingtin contains polyglutamine at its N-terminus and the yeast prion Sup35 protein has the GNNQQNY sequence, a peptide well-known for its ability for amyloid fibril formation. However, despite the frequent emergence of glutamine in self-assembling systems, the molecular mechanism of amyloid formation involving this unique amino acid has not been well documented. It is still not clear how this hydrophilic amino acid is responsible for the hydrophobic interaction in the self-association process. Therefore, in this study, we have carried out classical molecular dynamics simulations of the GNNQQNY peptide and its derivatives in pure water. We quantify the propensity for the formation of β-sheet conformation with an increasing glutamine number in the peptide sequence. In addition, we assess the importance of the hydrophobicity of the dimethanediyl group present in glutamine (as well as in glutamic acid) for the self-association of the peptides through nonpolar solvent medium simulations.
Collapse
Affiliation(s)
- Srijita Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Komal Kumari
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| |
Collapse
|
8
|
Siu HW, Heck B, Kovermann M, Hauser K. Template-assisted design of monomeric polyQ models to unravel the unique role of glutamine side chains in disease-related aggregation. Chem Sci 2020; 12:412-426. [PMID: 33552461 PMCID: PMC7863018 DOI: 10.1039/d0sc05299j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/28/2020] [Indexed: 01/28/2023] Open
Abstract
PolyQ model peptides reveal the effect of individual glutamine side chains on fibril formation.
Expanded polyglutamine (polyQ) sequences cause numerous neurodegenerative diseases which are accompanied by the formation of polyQ fibrils. The unique role of glutamines in the aggregation onset is undoubtedly accepted and a lot structural data of the fibrils have been acquired, however side-chain specific structural dynamics inducing oligomerization are not well understood yet. To analyze spectroscopically the nucleation process, we designed various template-assisted glutamine-rich β-hairpin monomers mimicking the structural motif of a polyQ fibril. In a top-down strategy, we use a template which forms a well-defined stable hairpin in solution, insert polyQ-rich sequences into each strand and monitor the effects of individual glutamines by NMR, CD and IR spectroscopic approaches. The design was further advanced by alternating glutamines with other amino acids (T, W, E, K), thereby enhancing the solubility and increasing the number of cross-strand interacting glutamine side chains. Our spectroscopic studies reveal a decreasing hairpin stability with increased glutamine content and demonstrate the enormous impact of only a few glutamines – far below the disease threshold – to destabilize structure. Furthermore, we could access sub-ms conformational dynamics of monomeric polyQ-rich peptides by laser-excited temperature-jump IR spectroscopy. Both, the increased number of interacting glutamines and higher concentrations are key parameters to induce oligomerization. Concentration-dependent time-resolved IR measurements indicate an additional slower kinetic phase upon oligomer formation. The here presented peptide models enable spectroscopic molecular analyses to distinguish between monomer and oligomer dynamics in the early steps of polyQ fibril formation and in a side-chain specific manner.
Collapse
Affiliation(s)
- Ho-Wah Siu
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Benjamin Heck
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Michael Kovermann
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Karin Hauser
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| |
Collapse
|
9
|
Smith NL, Coukouma AE, Jakubek RS, Asher SA. Mechanisms by Which Organic Solvent Exchange Transforms Responsive Pure Protein Hydrogels into Responsive Organogels. Biomacromolecules 2019; 21:839-853. [DOI: 10.1021/acs.biomac.9b01522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Natasha Lynn Smith
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Andrew Eagle Coukouma
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ryan S. Jakubek
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
10
|
Tian KZ, Cao CC, Nie XM, Wang W, Han CQ. Sensitive and label-free detection of protein secondary structure by amide III spectral signals using surface-enhanced Raman spectroscopy. CHINESE J CHEM PHYS 2019. [DOI: 10.1063/1674-0068/cjcp1811267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kang-zhen Tian
- Jiangsu Key Laboratory of Advanced Laser Materials and Devices, School of Physics and Electronic Engineering, Jiangsu Normal University, Xuzhou 221116, China
| | - Chang-chun Cao
- The 95979 Army of Chinese People’s Liberation Army, Taian 271200, China
| | - Xin-ming Nie
- Jiangsu Key Laboratory of Advanced Laser Materials and Devices, School of Physics and Electronic Engineering, Jiangsu Normal University, Xuzhou 221116, China
| | - Wen Wang
- Jiangsu Key Laboratory of Advanced Laser Materials and Devices, School of Physics and Electronic Engineering, Jiangsu Normal University, Xuzhou 221116, China
| | - Cai-qin Han
- Jiangsu Key Laboratory of Advanced Laser Materials and Devices, School of Physics and Electronic Engineering, Jiangsu Normal University, Xuzhou 221116, China
| |
Collapse
|
11
|
Graefe CT, Punihaole D, Harris CM, Lynch MJ, Leighton R, Frontiera RR. Far-Field Super-Resolution Vibrational Spectroscopy. Anal Chem 2019; 91:8723-8731. [PMID: 31251563 DOI: 10.1021/acs.analchem.9b01731] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Potential label-free alternatives to super-resolution fluorescence techniques have been the focus of considerable research due to the challenges intrinsic in the reliance on fluorescent tags. In this Feature, we discuss efforts to develop super-resolution techniques based on vibrational spectroscopies and address possible sample applications as well as future potential resolution enhancements.
Collapse
Affiliation(s)
- Christian T Graefe
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - David Punihaole
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Celina M Harris
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Michael J Lynch
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Ryan Leighton
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Renee R Frontiera
- Department of Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| |
Collapse
|
12
|
Jakubek RS, Workman RJ, White SE, Asher SA. Polyglutamine Solution-State Structural Propensity Is Repeat Length Dependent. J Phys Chem B 2019; 123:4193-4203. [PMID: 31008597 DOI: 10.1021/acs.jpcb.9b01433] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Expanded polyglutamine (polyQ) tracts in proteins, which are known to induce their aggregation, are associated with numerous neurodegenerative diseases. Longer polyQ tracts correlate with faster protein aggregation kinetics and a decreased age of onset for polyQ disease symptoms. Here, we use UV resonance Raman spectroscopy, circular dichroism spectroscopy, and metadynamics simulations to investigate the solution-state structures of the D2Q15K2 (Q15) and D2Q20K2 (Q20) peptides. Using metadynamics, we explore the conformational energy landscapes of Q15 and Q20 and investigate the relative energies and activation barriers between these low-energy structures. We compare the solution-state structures of D2Q10K2 (Q10), Q15, and Q20 to determine the dependence of polyQ structure on the Q tract length. We show that these peptides can adopt two distinct monomeric conformations: an aggregation-resistant PPII-like conformation and an aggregation-prone β-strand-like conformation. We find that longer polyQ peptides have an increased preference for the aggregation-prone β-strand-like conformation. This preference may play an important role in the increased aggregation rate of longer polyQ peptides that is thought to lead to decreased neurodegenerative disease age of onset for polyQ disease patients.
Collapse
Affiliation(s)
| | - Riley J Workman
- Department of Chemistry and Biochemistry, Center for Computational Sciences , Duquesne University , Pittsburgh , Pennsylvania 15282 , United States
| | | | | |
Collapse
|
13
|
Jakubek RS, White SE, Asher SA. UV Resonance Raman Structural Characterization of an (In)soluble Polyglutamine Peptide. J Phys Chem B 2019; 123:1749-1763. [PMID: 30717595 DOI: 10.1021/acs.jpcb.8b10783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fibrillization of polyglutamine (polyQ) tracts in proteins is implicated in at least 10 neurodegenerative diseases. This generates great interest in the structure and the aggregation mechanism(s) of polyQ peptides. The fibrillization of polyQ is thought to result from the peptide's insolubility in aqueous solutions; longer polyQ tracts show decreased aqueous solution solubility, which is thought to lead to faster fibrillization kinetics. However, few studies have characterized the structure(s) of polyQ peptides with low solubility. In the work here, we use UV resonance Raman spectroscopy to examine the secondary structures, backbone hydrogen bonding, and side chain hydrogen bonding for a variety of solution-state, solid, and fibril forms of D2Q20K2 (Q20). Q20 is insoluble in water and has a β-strand-like conformation with extensive inter- and intrapeptide hydrogen bonding in both dry and aqueous environments. We find that Q20 has weaker backbone-backbone and backbone-side chain hydrogen bonding and is less ordered compared to that of polyQ fibrils. Interestingly, we find that the insoluble Q20 will form fibrils when incubated in water at room temperature for ∼5 h. Also, Q20 can be prepared using a well-known disaggregation procedure to produce a water-soluble PPII-like conformation with negligible inter- and intrapeptide hydrogen bonding and a resistance to aggregation.
Collapse
|
14
|
Chen Y, Xing Z, Liao D, Qiu F. Neglected Hydrophobicity of Dimethanediyl Group in Peptide Self-Assembly: A Hint from Amyloid-like Peptide GNNQQNY and Its Derivatives. J Phys Chem B 2018; 122:10470-10477. [PMID: 30372075 DOI: 10.1021/acs.jpcb.8b09220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Besides typical hydrophobic amino acids providing hydrophobic interactions, glutamine as a hydrophilic amino acid has also been known to be an important element in many self-assembling peptides, but it is still not clear how this particular amino acid contributes to the self-assembling process. We supposed that the dimethanediyl group in the side chain of glutamine could provide hydrophobic interaction for peptide self-assembly. To prove this hypothesis, we used the GNNQQNY peptide and its derivatives as examples to show the importance of the dimethanediyl group for peptide self-assembly. We found a very close relationship between the number of dimethanediyl groups, the strength of hydrophobic interaction, and the self-assembling ability of the peptides, indicating the hydrophobicity of the dimethanediyl group and its important role for self-assembly. This new finding might be instructive for clarifying the self-assembling mechanism of many natural peptides, as well as for developing novel self-assembling peptide nanomaterials.
Collapse
|
15
|
Punihaole D, Workman RJ, Upadhyay S, Bruggen CV, Schmitz AJ, Reineke TM, Frontiera RR. New Insights into Quinine-DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations. J Phys Chem B 2018; 122:9840-9851. [PMID: 30336027 PMCID: PMC6425490 DOI: 10.1021/acs.jpcb.8b05795] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Quinine's ability to bind DNA and potentially inhibit transcription and translation has been examined as a mode of action for its antimalarial activity. UV absorption and fluorescence-based studies have lacked the chemical specificity to develop an unambiguous molecular-level picture of the binding interaction. To address this, we use Raman spectroscopy and molecular dynamics (MD) to investigate quinine-DNA interactions. We demonstrate that quinine's strongest Raman band in the fingerprint region, which derives from a symmetric stretching mode of the quinoline ring, is highly sensitive to the local chemical environment and pH. The frequency shifts observed for this mode in solvents of varying polarity can be explained in terms of the Stark effect using a simple Onsager solvation model, indicating that the vibration reports on the local electrostatic environment. However, specific chemical interactions between the quinoline ring and its environment, such as hydrogen bonding and π-stacking, perturb the frequency of this mode in a more complicated but predictable manner. We use this vibration as a spectroscopic probe to investigate the binding interaction between quinine and DNA. We find that, when the quinoline ring is protonated, quinine weakly intercalates into DNA by forming π-stacking interactions with the base pairs. The Raman spectra indicate that quinine can intercalate into DNA with a ratio reaching up to roughly one molecule per 25 base pairs. Our results are confirmed by MD simulations, which also show that the quinoline ring adopts a t-shaped π-stacking geometry with the DNA base pairs, whereas the quinuclidine head group weakly interacts with the phosphate backbone in the minor groove. We expect that the spectral correlations determined here will enable future studies to probe quinine's antimalarial activities, such as disrupting hemozoin biocrystallization, which is hypothesized to be, among other things, one of its primary modes of action against Plasmodium parasites.
Collapse
Affiliation(s)
- David Punihaole
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Riley J. Workman
- Department of Chemistry and Biochemistry, Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Shiv Upadhyay
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Craig Van Bruggen
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andrew J. Schmitz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M. Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Renee R. Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|