1
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Cheeseman JR, Frisch MJ, Keiderling TA. Increased accuracy of vibrational circular dichroism calculations for isotopically labeled helical peptides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124097. [PMID: 38457873 DOI: 10.1016/j.saa.2024.124097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
Vibrational circular dichroism (VCD) spectra have been computed with qualitatively correct sign patterns for α-helical peptides using various methods, ranging from empirical models to ab initio quantum mechanical computations. However, some details, such as deuteration effects and isotope substitution shifts and sign patterns for the resultant amide I' band shape, have remained a predictive challenge. Fully optimized computations for a 25-residue Ala-rich peptide, including implicit solvent corrections and explicit side chains that experimentally stabilize these model helical peptides in water, have been carried out using density functional theory (DFT). These fully minimized structures show minor changes in the (ϕ,ψ) torsions at the termini and yield an extra negative band to the low energy side of the characteristic amide I' couplet VCD, in agreement with experiments. Additionally, these calculations give the right sign and relative intensity patterns, as compared to experimental results, for several 13C=O substituted variants. The differences from previously reported computations that used ideal helical structures and vacuum conditions imply that inclusion of distorted termini and solvent effects can have an impact on the final detailed spectral patterns. Inclusion of side chains in these calculations had very little effect on the computed amide I' IR and VCD. Tests of constrained geometries, varying dielectric, and different functionals indicate that each can affect the band shapes, particularly for the 12C=O components, but these aspects do not fully explain the difference from previous spectral simulations. Inclusion of long-range amide coupling, as obtained from DFT computation of the full structure, or transfer of parameters from a somewhat longer peptide model, rather than shorter model, seems to be more important for the final detailed band shape under isotopic substitution. However, these corrections can also induce other changes, suggesting that previously reported, limited calculations may have been qualitatively useful due to a balance of errors. This may also explain the success of simple empirical IR models.
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Affiliation(s)
- James R Cheeseman
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492, USA
| | - Michael J Frisch
- Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492, USA
| | - Timothy A Keiderling
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA.
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2
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Majka Z, Kwiecień K, Kaczor A. Vibrational Optical Activity of Amyloid Fibrils. Chempluschem 2024:e202400091. [PMID: 38421108 DOI: 10.1002/cplu.202400091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/02/2024]
Abstract
Amyloid fibrils are supramolecular systems showing distinct chirality at different levels of their complex multilayered architectures. Due to the regular long-range chiral organization, amyloid fibrils exhibit the most intense Vibrational Optical Activity (VOA) signal observed up to now, making VOA techniques: Vibrational Circular Dichroism (VCD) and Raman Optical Activity (ROA) very promising tools to explore their structures, handedness and intricate polymorphism. This concept article reviews up-to-date experimental studies on VOA applications to investigate amyloid fibrils highlighting its future potential in analyzing of these unique supramolecular systems, in particular in the context of biomedicine and nanotechnology.
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Affiliation(s)
- Zuzanna Majka
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387, Krakow, Poland
| | - Karolina Kwiecień
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387, Krakow, Poland
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Prof. St. Łojasiewicza 11 Str., Krakow, Poland
- Łukasiewicz Research Network-Institute of Microelectronics and Photonics, 39 Zabłocie Str., 30-701, Krakow, Poland
| | - Agnieszka Kaczor
- Faculty of Chemistry, Jagiellonian University, 2 Gronostajowa Str., 30-387, Krakow, Poland
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3
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Dec R, Okoń R, Puławski W, Wacławska M, Dzwolak W. Forced amyloidogenic cooperativity of structurally incompatible peptide segments: Fibrillization behavior of highly aggregation-prone A-chain fragment of insulin coupled to all-L, and alternating L/D octaglutamates. Int J Biol Macromol 2022; 223:362-369. [PMID: 36368353 DOI: 10.1016/j.ijbiomac.2022.11.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/06/2022] [Indexed: 11/10/2022]
Abstract
Aggregation of proteins into amyloid fibrils is driven by interactions between relatively small amyloidogenic segments. The interplay between aggregation-prone and aggregation-resistant fragments within a single polypeptide chain remains obscure. Here, we examine fibrillization behavior of two chimeric peptides, ACC1-13E8 and ACC1-13E8(L/D), in which the highly amyloidogenic fragment of insulin (ACC1-13) is extended by an octaglutamate segment composed of all-L (E8), or alternating L/D residues (E8(L/D)). As separate entities, ACC1-13 readily forms fibrils with the infrared features of parallel β-sheet while E8 forms antiparallel β-sheets with the distinct infrared characteristics. This contrasts with the profoundly aggregation-resistant E8(L/D), although L/D patterns have been hypothesized as compatible with aggregated α-sheets. ACC1-13E8 and ACC1-13E8(L/D) are found to be equally prone to fibrillization at low pH, or in the presence of Ca2+ ions. Fibrillar states of both ACC1-13E8 and ACC1-13E8(L/D) reveal the infrared features of highly ordered parallel β-sheet without evidence of β2-aggregates (ACC1-13E8) or α-sheets (ACC1-13E8(L/D)). Hence, the preferred structural pattern of ACC1-13 overrides the tendency of E8 to form antiparallel β-sheets and enforces the fibrillar order in E8(L/D). We demonstrate how the powerful amyloid stretch determines the overall amyloid structure forcing non-amyloidogenic fragments to participate in its native amyloid pattern.
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Affiliation(s)
- Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, 02-093 Warsaw, Poland
| | - Róża Okoń
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, 02-093 Warsaw, Poland
| | - Wojciech Puławski
- Bioinformatics Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego Street 5, 02-106 Warsaw, Poland
| | - Matylda Wacławska
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, 02-093 Warsaw, Poland
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur Street 1, 02-093 Warsaw, Poland; Institute of High Pressure Physics, Polish Academy of Sciences, Sokołowska Street 29/37, 01-142 Warsaw, Poland.
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4
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Eikås KDR, Beerepoot MTP, Ruud K. A Computational Protocol for Vibrational Circular Dichroism Spectra of Cyclic Oligopeptides. J Phys Chem A 2022; 126:5458-5471. [PMID: 35930395 PMCID: PMC9393892 DOI: 10.1021/acs.jpca.2c02953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic peptides are a promising class of compounds for next-generation antibiotics as they may provide new ways of limiting antibiotic resistance development. Although their cyclic structure will introduce some rigidity, their conformational space is large and they usually have multiple chiral centers that give rise to a wide range of possible stereoisomers. Chiroptical spectroscopies such as vibrational circular dichroism (VCD) are used to assign stereochemistry and discriminate enantiomers of chiral molecules, often in combination with electronic structure methods. The reliable determination of the absolute configuration of cyclic peptides will require robust computational methods than can identify all significant conformers and their relative population and reliably assign their stereochemistry from their chiroptical spectra by comparison with ab initio calculated spectra. We here present a computational protocol for the accurate calculation of the VCD spectra of a series of flexible cyclic oligopeptides. The protocol builds on the Conformer-Rotamer Ensemble Sampling Tool (CREST) developed by Grimme and co-workers ( Phys. Chem. Chem. Phys. 2020, 22, 7169-7192 and J. Chem. Theory. Comput. 2019, 15, 2847-2862) in combination with postoptimizations using B3LYP and moderately sized basis sets. Our recommended computational protocol for the computation of VCD spectra of cyclic oligopeptides consists of three steps: (1) conformational sampling with CREST and tight-binding density functional theory (xTB); (2) energy ranking based on single-point energy calculations as well as geometry optimization and VCD calculations of conformers that are within 2.5 kcal/mol of the most stable conformer using B3LYP/6-31+G*/CPCM; and (3) VCD spectra generation based on Boltzmann weighting with Gibbs free energies. Our protocol provides a feasible basis for generating VCD spectra also for larger cyclic peptides of biological/pharmaceutical interest and can thus be used to investigate promising compounds for next-generation antibiotics.
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Affiliation(s)
- Karolina Di Remigio Eikås
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Maarten T P Beerepoot
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.,Norwegian Defence Research Establishment, P.O. Box 25, 2027 Kjeller, Norway
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5
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Krupová M, Kessler J, Bouř P. Polymorphism of Amyloid Fibrils Induced by Catalytic Seeding: A Vibrational Circular Dichroism Study. Chemphyschem 2020; 22:83-91. [DOI: 10.1002/cphc.202000797] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/16/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Mathematics and Physics Charles University Ke Karlovu 3 12116 Prague 2 Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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6
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Dec R, Guza M, Dzwolak W. Reduction of a disulfide-constrained oligo-glutamate peptide triggers self-assembly of β 2-type amyloid fibrils with the chiroptical properties determined by supramolecular chirality. Int J Biol Macromol 2020; 162:866-872. [PMID: 32593758 DOI: 10.1016/j.ijbiomac.2020.06.221] [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: 03/29/2020] [Revised: 06/15/2020] [Accepted: 06/23/2020] [Indexed: 11/27/2022]
Abstract
Disulfide bonds prevent aggregation of globular proteins by stabilizing the native state. However, a disulfide bond within a disordered state may accelerate amyloidogenic nucleation by navigating fluctuating polypeptide chains towards an orderly assembly of β-sheets. Here, the self-assembly behavior of Glu-Cys-(Glu)4-Cys-Glu peptide (E6C2), in which an intrachain disulfide bond is engineered into an amyloidogenic homopolypeptide motif, is investigated. To this end, the Thioflavin T (ThT) fluorescence kinetic assay is combined with infrared spectroscopy, circular dichroism (CD), atomic force microscopy (AFM) and Raman scattering measurements. Regardless of whether the disulfide bond is intact or reduced, E6C2 monomers remain disordered within a broad range of pH. On the other hand, only reduced E6C2 self-assembles into amyloid fibrils with the unique infrared traits indicative of three-center hydrogen bonds involving main-chain carbonyl as a bifurcating acceptor and main-chain NH and side-chain -COOH groups as hydrogen donors: the bonding pattern observed in so-called β2-fibrils. AFM analysis of β2-E6C2 reveals tightly packed rectangular superstructures whose presence coincides with strong chiroptical properties. Our findings suggest that formation of chiral amyloid superstructures may be a generic process accessible to various substrates, and that the fully extended conformation of a poly-Glu chain is a condition sine qua non for self-assembly of β2-fibrils.
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Affiliation(s)
- Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Str., 02-093 Warsaw, Poland
| | - Marcin Guza
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Str., 02-093 Warsaw, Poland
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Str., 02-093 Warsaw, Poland.
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7
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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8
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Mello LR, Hamley IW, Miranda A, Alves WA, Silva ER. β
‐
sheet assembly in amyloidogenic glutamic acid nanostructures: Insights from X‐ray scattering and infrared nanospectroscopy. J Pept Sci 2019; 25:e3170. [DOI: 10.1002/psc.3170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Lucas R. Mello
- Departamento de BiofísicaUniversidade Federal de São Paulo São Paulo Brazil
| | - Ian W. Hamley
- Department of ChemistryUniversity of Reading Reading UK
| | - Antonio Miranda
- Departamento de BiofísicaUniversidade Federal de São Paulo São Paulo Brazil
| | - Wendel A. Alves
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABC Santo André Brazil
| | - Emerson R. Silva
- Departamento de BiofísicaUniversidade Federal de São Paulo São Paulo Brazil
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9
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Krupová M, Kapitán J, Bouř P. Induced Lanthanide Circularly Polarized Luminescence as a Probe of Protein Fibrils. ACS OMEGA 2019; 4:1265-1271. [PMID: 31459399 PMCID: PMC6648570 DOI: 10.1021/acsomega.8b03175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/27/2018] [Indexed: 06/10/2023]
Abstract
Protein fibrils are involved in a number of biological processes. Because their structure is very complex and not completely understood, different spectroscopic methods are used to monitor different aspects of fibril structure. We have explored circularly polarized luminescence (CPL) induced in lanthanide compounds to indicate fibril growth and discriminate among fibril types. For hen egg-white lysozyme and polyglutamic acid-specific CPL, spectral patterns were obtained and could be correlated with vibrational circular dichroism (VCD) spectra and thioflavin T fluorescence. The CPL spectra were measured on a Raman optical activity spectrometer, and its various polarization modes are discussed. The experiments indicate that the induced CPL is sensitive to more local aspects of the fibril structure than VCD. For CPL, smaller amounts of the sample are required for the analysis, and thus this method appears to be a good candidate for future spectroscopic characterization of these peptide and protein aggregates.
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Affiliation(s)
- Monika Krupová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí
2, 16610 Prague, Czech Republic
- Faculty
of Mathematics and Physics, Charles University, Ke Karlovu 3, 12116 Prague 2, Czech Republic
| | - Josef Kapitán
- Department
of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí
2, 16610 Prague, Czech Republic
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10
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Vibrational Approach to the Dynamics and Structure of Protein Amyloids. Molecules 2019; 24:molecules24010186. [PMID: 30621325 PMCID: PMC6337179 DOI: 10.3390/molecules24010186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/31/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Amyloid diseases, including neurodegenerative diseases such as Alzheimer’s and Parkinson’s, are linked to a poorly understood progression of protein misfolding and aggregation events that culminate in tissue-selective deposition and human pathology. Elucidation of the mechanistic details of protein aggregation and the structural features of the aggregates is critical for a comprehensive understanding of the mechanisms of protein oligomerization and fibrillization. Vibrational spectroscopies, such as Fourier transform infrared (FTIR) and Raman, are powerful tools that are sensitive to the secondary structure of proteins and have been widely used to investigate protein misfolding and aggregation. We address the application of the vibrational approaches in recent studies of conformational dynamics and structural characteristics of protein oligomers and amyloid fibrils. In particular, introduction of isotope labelled carbonyl into a peptide backbone, and incorporation of the extrinsic unnatural amino acids with vibrational moieties on the side chain, have greatly expanded the ability of vibrational spectroscopy to obtain site-specific structural and dynamic information. The applications of these methods in recent studies of protein aggregation are also reviewed.
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11
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Berbeć S, Dec R, Molodenskiy D, Wielgus-Kutrowska B, Johannessen C, Hernik-Magoń A, Tobias F, Bzowska A, Ścibisz G, Keiderling TA, Svergun D, Dzwolak W. β2-Type Amyloidlike Fibrils of Poly-l-glutamic Acid Convert into Long, Highly Ordered Helices upon Dissolution in Dimethyl Sulfoxide. J Phys Chem B 2018; 122:11895-11905. [DOI: 10.1021/acs.jpcb.8b08308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sylwia Berbeć
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Dmitry Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | | | - Agnieszka Hernik-Magoń
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw 02-093, Poland
| | - Grzegorz Ścibisz
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago 60607-7061, United States
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Hamburg 22607, Germany
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
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12
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Instrumentation for Vibrational Circular Dichroism Spectroscopy: Method Comparison and Newer Developments. Molecules 2018; 23:molecules23092404. [PMID: 30235902 PMCID: PMC6225159 DOI: 10.3390/molecules23092404] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 08/25/2018] [Accepted: 09/07/2018] [Indexed: 01/10/2023] Open
Abstract
Vibrational circular dichroism (VCD) is a widely used standard method for determination of absolute stereochemistry, and somewhat less so for biomolecule characterization and following dynamic processes. Over the last few decades, different VCD instrument designs have developed for various purposes, and reliable commercial instrumentation is now available. This review will briefly survey historical and currently used instrument designs and describe some aspects of more recently reported developments. An important factor in applying VCD to conformational studies is theoretical modeling of spectra for various structures, techniques for which are briefly surveyed.
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13
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Keiderling TA, Lakhani A. Mini review: Instrumentation for vibrational circular dichroism spectroscopy, still a role for dispersive instruments. Chirality 2018; 30:238-253. [PMID: 29293282 DOI: 10.1002/chir.22799] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/07/2017] [Accepted: 11/16/2017] [Indexed: 01/30/2023]
Abstract
Vibrational circular dichroism (VCD) has become a standard method for determination of absolute stereochemistry, particularly now that reliable commercial instrumentation has become available. These instruments use a now well-documented Fourier transform infrared-based approach to measure VCD that has virtually displaced initial dispersive infrared-based designs. Nonetheless, many papers have appeared reporting dispersive VCD data, especially for biopolymers. Instrumentation designed with these original methods, particularly after more recent updates optimizing performance in selected spectral regions, has been shown still to have advantages for specific applications. This article presents a mini-review of dispersive VCD instrument designs and includes sample spectra obtained for various biopolymer (particularly peptide) samples. Complementary reviews of Fourier transform-VCD designs are broadly available.
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Affiliation(s)
- Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ahmed Lakhani
- Department of Biophysical Chemistry and Mathematics, Calumet College of St. Joseph, Whiting, Indiana, USA
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14
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Serrano AL, Lomont JP, Tu LH, Raleigh DP, Zanni MT. A Free Energy Barrier Caused by the Refolding of an Oligomeric Intermediate Controls the Lag Time of Amyloid Formation by hIAPP. J Am Chem Soc 2017; 139:16748-16758. [PMID: 29072444 DOI: 10.1021/jacs.7b08830] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F23G24A25I26L27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.
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Affiliation(s)
- Arnaldo L Serrano
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Ling-Hsien Tu
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11790, United States
| | - Daniel P Raleigh
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11790, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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15
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Keiderling TA. Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides. Chirality 2017; 29:763-773. [DOI: 10.1002/chir.22749] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/07/2022]
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16
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Hernik-Magoń A, Fedorczyk B, Dec R, Puławski W, Misicka A, Dzwolak W. Effects of terminal capping on the fibrillation of short (L-Glu) n peptides. Colloids Surf B Biointerfaces 2017; 159:861-868. [PMID: 28892870 DOI: 10.1016/j.colsurfb.2017.08.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/23/2017] [Accepted: 08/30/2017] [Indexed: 02/07/2023]
Abstract
Several homopolypeptides including poly-l-glutamic acid (PLGA) form amyloid-like fibrils under favorable physicochemical conditions. We have shown recently that even short uncapped (Glu)n peptides (for n>3) form fibrillar β-aggregates which cross-seed with amyloid fibrils obtained from high molecular weight fractions of PLGA. Here we investigate effects of N-terminal acetylation and C-terminal amidation on the amyloidogenic tendencies of (Glu)n peptides containing 3, 4, and 5 residues. Our results based primarily on time-lapse FT-IR spectroscopy and AFM microscopy indicate that selective modifications of C-termini (and, to a lesser degree, of N-termini) decrease capacity of tetra- and pentapeptides to form fibrils. On the other hand, peptides modified at both ends appear to form fibrils as fast as unmodified analogues. In fact, the double terminal modification enables fibrillation of (Glu)3 which is not fibrillogenic in the unmodified state. The AFM data suggests that the double capping results in the aggregates becoming more tape-like or acquiring noticeable tendencies to bend. According to seeding and cross-seeding experiments, there is a high degree of promiscuity between modified and unmodified peptides. Possible mechanisms explaining how amyloidogenic propensities of (Glu)n peptides are affected by terminal modifications have been discussed.
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Affiliation(s)
- Agnieszka Hernik-Magoń
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 St., 02-093 Warsaw, Poland
| | - Bartłomiej Fedorczyk
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 St., 02-093 Warsaw, Poland
| | - Robert Dec
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 St., 02-093 Warsaw, Poland
| | - Wojciech Puławski
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 St., 02-093 Warsaw, Poland
| | - Aleksandra Misicka
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 St., 02-093 Warsaw, Poland
| | - Wojciech Dzwolak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteur 1 St., 02-093 Warsaw, Poland.
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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18
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Chang C, Liang P, Chen L, Liu J, Chen S, Zheng G, Quan C. pH-responsive nanoparticle assembly from peptide amphiphiles for tumor targeting drug delivery. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2017; 28:1338-1350. [PMID: 28467173 DOI: 10.1080/09205063.2017.1325095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In this paper, the peptide amphiphiles (PA) which consists of RGDSEEEEEEEEEEK as pH-sensitive segment and stearic acid as hydrophobic segment named RGDS-E10-Lys(C18) was successfully synthesized. TEM images showed that uniformly dispersed nanoparticles could be formed by PA molecules in pH 7.4 medium, however, disintegrated in pH 5.0 medium. Circular dichroism (CD) spectrum indicated that polypeptide adopted a random-coil conformation in neutral medium (pH 7.4). The CD signal was significantly attenuate for decreased solubility of PA in medium with pH 5.0. As expected, the prepared RGDS-E10-Lys(C18) assembly showed high pH-sensitive property which demonstrated a much more rapid drug release from micelles in tumor tissue (acidic environment) than in physiological environment (neutral environment). After DOX-loaded micelles incubated with tumor cells, the cytotoxicity of the micelles against Hela cells was increased obviously, indicating the great potential of micelles developed here as promising vehicle for targeted pH-responsive drug delivery.
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Affiliation(s)
- Cong Chang
- a Key Laboratory of Chinese Medicine Resource and Compound Prescription of Ministry of Education , Hubei University of Chinese Medicine , Wuhan , P. R. China
| | - Peiqing Liang
- b Department of Biomedical Engineering , School of Engineering, Sun Yat-sen University , Guangzhou , P. R. China
| | - Linlin Chen
- a Key Laboratory of Chinese Medicine Resource and Compound Prescription of Ministry of Education , Hubei University of Chinese Medicine , Wuhan , P. R. China
| | - Junfeng Liu
- a Key Laboratory of Chinese Medicine Resource and Compound Prescription of Ministry of Education , Hubei University of Chinese Medicine , Wuhan , P. R. China
| | - Shihong Chen
- a Key Laboratory of Chinese Medicine Resource and Compound Prescription of Ministry of Education , Hubei University of Chinese Medicine , Wuhan , P. R. China
| | - Guohua Zheng
- a Key Laboratory of Chinese Medicine Resource and Compound Prescription of Ministry of Education , Hubei University of Chinese Medicine , Wuhan , P. R. China
| | - Changyun Quan
- b Department of Biomedical Engineering , School of Engineering, Sun Yat-sen University , Guangzhou , P. R. China
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19
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Chi H, Keiderling TA. Structural Rearrangement from Oligomer to Fibril Detected with FRET in a Designed Amphiphilic Peptide. Chembiochem 2016; 18:195-205. [DOI: 10.1002/cbic.201600436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Heng Chi
- Department of Chemistry (M/C 111); University of Illinois at Chicago; 845 W. Taylor Street Chicago IL 60607 USA
- Department of Pharmacy; Jiangsu Food and Pharmaceutical Science College; 4 E. Meicheng Rd. Huai'an Jiangsu Province 223005 China
| | - Timothy A. Keiderling
- Department of Chemistry (M/C 111); University of Illinois at Chicago; 845 W. Taylor Street Chicago IL 60607 USA
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20
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Tobias F, Keiderling TA. Role of Side Chains in β-Sheet Self-Assembly into Peptide Fibrils. IR and VCD Spectroscopic Studies of Glutamic Acid-Containing Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:4653-61. [PMID: 27099990 DOI: 10.1021/acs.langmuir.6b00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Poly(glutamic acid) at low pH self-assembles after incubation at higher temperature into fibrils composed of antiparallel sheets that are stacked in a β2-type structure whose amide carbonyls have bifurcated H-bonds involving the side chains from the next sheet. Oligomers of Glu can also form such structures, and isotope labeling has provided insight into their out-of-register antiparallel structure [ Biomacromolecules 2013 , 14 , 3880 - 3891 ]. In this paper we report IR and VCD spectra and transmission electron micrograph (TEM) images for a series of alternately sequenced oligomers, Lys-(Aaa-Glu)5-Lys-NH2, where Aaa was varied over a variety of polar, aliphatic, or aromatic residues. Their spectral and TEM data show that these oligopeptides self-assemble into different structures, both local and morphological, that are dependent on both the nature of the Aaa side chains and growth conditions employed. Such alternate peptides substituted with small or polar residues, Ala and Thr, do not yield fibrils; but with β-branched aliphatic residues, Val and Ile, that could potentially pack with Glu side chains, these oligopeptides do show evidence of β2-stacking. By contrast, for Leu, with longer side chains, only β1-stacking is seen while with even larger Phe side chains, either β-form can be detected separately, depending on preparation conditions. These structures are dependent on high temperature incubation after reducing the pH and in some cases after sonication of initial fibril forms and reincubation. Some of these fibrillar peptides, but not all, show enhanced VCD, which can offer evidence for formation of long, multistrand, often twisted structures. Substitution of Glu with residues having selected side chains yields a variety of morphologies, leading to both β1- and β2-structures, that overall suggests two different packing modes for the hydrophobic side chains depending on size and type.
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Affiliation(s)
- Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago , 845 W. Taylor Street (m/c111), Chicago, Illinois 60607-7061, United States
| | - Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago , 845 W. Taylor Street (m/c111), Chicago, Illinois 60607-7061, United States
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21
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Hernik-Magoń A, Puławski W, Fedorczyk B, Tymecka D, Misicka A, Szymczak P, Dzwolak W. Beware of Cocktails: Chain-Length Bidispersity Triggers Explosive Self-Assembly of Poly-L-Glutamic Acid β2-Fibrils. Biomacromolecules 2016; 17:1376-82. [PMID: 26909651 DOI: 10.1021/acs.biomac.5b01770] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Chain-length polydispersity is among the least understood factors governing the fibrillation propensity of homopolypeptides. For monodisperse poly-L-glutamic acid (PLGA), the tendency to form fibrils depends of the main-chain length. Long-chained PLGA, so-called (Glu)200, fibrillates more readily than short (Glu)5 fragments. Here we show that conversion of α-helical (Glu)200 into amyloid-like β-fibrils is dramatically accelerated in the presence of intrinsically disordered (Glu)5. While separately self-assembled fibrils of (Glu)200 and (Glu)5 reveal distinct morphological and infrared characteristics, accelerated fibrillation in mixed (Glu)200 and (Glu)5 leads to aggregates similar to neat (Glu)200 fibrils, even in excess of (Glu)5. According to molecular dynamics simulations and circular dichroism measurements, local events of "misfolding transfer" from (Glu)5 to (Glu)200 may play a key role in the initial stages of conformational dynamics underlying the observed phenomenon. Our results highlight chain-length polydispersity as a potent, although so-far unrecognized factor profoundly affecting the fibrillation propensity of homopolypeptides.
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Affiliation(s)
- Agnieszka Hernik-Magoń
- Department of Chemistry, Biological and Chemical Research Centre, and ‡Institute of Theoretical Physics, Faculty of Physics, University of Warsaw , Warsaw, Poland
| | - Wojciech Puławski
- Department of Chemistry, Biological and Chemical Research Centre, and ‡Institute of Theoretical Physics, Faculty of Physics, University of Warsaw , Warsaw, Poland
| | - Bartłomiej Fedorczyk
- Department of Chemistry, Biological and Chemical Research Centre, and ‡Institute of Theoretical Physics, Faculty of Physics, University of Warsaw , Warsaw, Poland
| | - Dagmara Tymecka
- Department of Chemistry, Biological and Chemical Research Centre, and ‡Institute of Theoretical Physics, Faculty of Physics, University of Warsaw , Warsaw, Poland
| | - Aleksandra Misicka
- Department of Chemistry, Biological and Chemical Research Centre, and ‡Institute of Theoretical Physics, Faculty of Physics, University of Warsaw , Warsaw, Poland
| | - Piotr Szymczak
- Department of Chemistry, Biological and Chemical Research Centre, and ‡Institute of Theoretical Physics, Faculty of Physics, University of Warsaw , Warsaw, Poland
| | - Wojciech Dzwolak
- Department of Chemistry, Biological and Chemical Research Centre, and ‡Institute of Theoretical Physics, Faculty of Physics, University of Warsaw , Warsaw, Poland
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22
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Zhang G, Babenko V, Dzwolak W, Keiderling TA. Dimethyl Sulfoxide Induced Destabilization and Disassembly of Various Structural Variants of Insulin Fibrils Monitored by Vibrational Circular Dichroism. Biochemistry 2015; 54:7193-202. [DOI: 10.1021/acs.biochem.5b00809] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ge Zhang
- Department
of Chemistry, University of Illinois at Chicago, 845 West Taylor
Street (m/c 111), Chicago, Illinois 60607-7061, United States
| | - Viktoria Babenko
- Department
of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Wojciech Dzwolak
- Department
of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Timothy A. Keiderling
- Department
of Chemistry, University of Illinois at Chicago, 845 West Taylor
Street (m/c 111), Chicago, Illinois 60607-7061, United States
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23
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Hernik A, Puławski W, Fedorczyk B, Tymecka D, Misicka A, Filipek S, Dzwolak W. Amyloidogenic Properties of Short α-L-Glutamic Acid Oligomers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10500-10507. [PMID: 26362583 DOI: 10.1021/acs.langmuir.5b02915] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Poly-L-glutamic acid (PLGA) forms amyloid-like β2-fibrils with the main spectral component of vibrational amide I' band unusually shifted below 1600 cm(-1). This distinct infrared feature has been attributed to the presence of bifurcated hydrogen bonds coupling C═O and N-D (N-H) groups of the main chains to glutamate side chains. Here, we investigate how decreasing the chain length of PLGA affects its capacity to form β2-fibrils. A series of acidified aqueous solutions of synthetic (l-Glu)n peptides (n ≈ 200, 10, 6, 5, 4, and 3) were incubated at high temperature. We observed that n = 4 is the critical chain length for which formation of aggregates with the β2-like infrared features is still observed under such conditions. Interestingly, according to atomic force microscopy (AFM), the self-assembly of (L-Glu)n chains varying vastly in length produces fibrils with rather uniform diameters of approximately 4-6 nm. Kinetic experiments on (L-Glu)5 and (L-Glu)200 peptides indicate that the fibrillation is significantly accelerated not only in the presence of homologous seeds but also upon cross-seeding, suggesting thereby a common self-assembly theme for (L-Glu)n chains of various lengths. Our results are discussed in the context of mechanisms of amyloidogenic fibrillation of homopolypeptides.
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Affiliation(s)
- Agnieszka Hernik
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Wojciech Puławski
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Bartłomiej Fedorczyk
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Dagmara Tymecka
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Aleksandra Misicka
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Sławomir Filipek
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
| | - Wojciech Dzwolak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw , 00-927 Warsaw, Poland
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24
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Sato H, Yajima T, Yamagishi A. Chiroptical Studies on Supramolecular Chirality of Molecular Aggregates. Chirality 2015; 27:659-66. [DOI: 10.1002/chir.22482] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Hisako Sato
- Graduated of Science and Engineering; Ehime University; Matsuyama Japan
| | - Tomoko Yajima
- Department of Chemistry; Ochanomizu University; Tokyo Japan
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25
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Nickels JD, Perticaroli S, Ehlers G, Feygenson M, Sokolov AP. Rigidity of poly-L-glutamic acid scaffolds: Influence of secondary and supramolecular structure. J Biomed Mater Res A 2015; 103:2909-18. [DOI: 10.1002/jbm.a.35427] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/13/2015] [Accepted: 02/04/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Jonathan D. Nickels
- Oak Ridge National Laboratory; Joint Institute for Neutron Sciences; Oak Ridge Tennessee 37831
- Department of Chemistry; University of Tennessee; Knoxville Tennessee 37996
| | - Stefania Perticaroli
- Oak Ridge National Laboratory; Joint Institute for Neutron Sciences; Oak Ridge Tennessee 37831
- Department of Chemistry; University of Tennessee; Knoxville Tennessee 37996
- Chemical and Materials Sciences Division; Oak Ridge National Laboratory; Oak Ridge Tennessee 37831
| | - Georg Ehlers
- Quantum Condensed Matter Division; Oak Ridge National Laboratory; Oak Ridge Tennessee 37831
| | - Mikhail Feygenson
- Chemical and Engineering Materials Division; Oak Ridge National Laboratory; Oak Ridge Tennessee 37831
| | - Alexei P. Sokolov
- Oak Ridge National Laboratory; Joint Institute for Neutron Sciences; Oak Ridge Tennessee 37831
- Department of Chemistry; University of Tennessee; Knoxville Tennessee 37996
- Chemical and Materials Sciences Division; Oak Ridge National Laboratory; Oak Ridge Tennessee 37831
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26
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Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:473-483. [PMID: 25036456 DOI: 10.1016/j.saa.2014.06.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/13/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
Studies of structural changes in peptides and proteins using IR spectroscopy often rely on subtle changes in the amide I' band as a function of temperature. However, these changes can be obscured by the overlap with other absorptions, namely the side-chain and terminal carboxylic groups. The former were the subject of our previous report (Anderson et al., 2014). In this paper we investigate the IR spectra of the asymmetric stretch of α-carboxylic groups for amino acids representing all major types (Gly, Ala, Val, Leu, Ser, Thr, Asp, Glu, Lys, Asn, His, Trp, Pro) as well as the C-terminal groups of three dipeptides (Gly-Gly, Gly-Ala, Ala-Gly) in D₂O at neutral pH. Experimental temperature dependent IR spectra were analyzed by fitting of both symmetric and asymmetric pseudo-Voigt functions. Qualitatively the spectra exhibit shifts to higher frequency, loss in intensity and narrowing with increased temperature, similar to that observed previously for the side-chain carboxylic groups of Asp. The observed dependence of the band parameters (frequency, intensity, width and shape) on temperature is in all cases linear: simple linear regression is therefore used to describe the spectral changes. The spectral parameters vary between individual amino acids and show systematic differences between the free amino acids and dipeptides, particularly in the absolute peak frequencies, but the temperature variations are comparable. The relative variations between the dipeptide spectral parameters are most sensitive to the C-terminal amino acid, and follow the trends observed in the free amino acid spectra. General rules for modeling the α-carboxylic IR absorption bands in peptides and proteins as the function of temperature are proposed.
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Affiliation(s)
- Benjamin A Anderson
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Alex Literati
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Borden Ball
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Jan Kubelka
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States.
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27
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Fulara A, Hernik A, Nieznańska H, Dzwolak W. Covalent defects restrict supramolecular self-assembly of homopolypeptides: case study of β2-fibrils of poly-L-glutamic acid. PLoS One 2014; 9:e105660. [PMID: 25144464 PMCID: PMC4140804 DOI: 10.1371/journal.pone.0105660] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 07/23/2014] [Indexed: 12/12/2022] Open
Abstract
Poly-L-glutamic acid (PLGA) often serves as a model in studies on amyloid fibrils and conformational transitions in proteins, and as a precursor for synthetic biomaterials. Aggregation of PLGA chains and formation of amyloid-like fibrils was shown to continue on higher levels of superstructural self-assembly coinciding with the appearance of so-called β2-sheet conformation manifesting in dramatic redshift of infrared amide I' band below 1600 cm(-1). This spectral hallmark has been attributed to network of bifurcated hydrogen bonds coupling C = O and N-D (N-H) groups of the main chains to glutamate side chains. However, other authors reported that, under essentially identical conditions, PLGA forms the conventional in terms of infrared characteristics β1-sheet structure (exciton-split amide I' band with peaks at ca. 1616 and 1683 cm(-1)). Here we attempt to shed light on this discrepancy by studying the effect of increasing concentration of intentionally induced defects in PLGA on the tendency to form β1/β2-type aggregates using infrared spectroscopy. We have employed carbodiimide-mediated covalent modification of Glu side chains with n-butylamine (NBA), as well as electrostatics-driven inclusion of polylysine chains, as two different ways to trigger structural defects in PLGA. Our study depicts a clear correlation between concentration of defects in PLGA and increasing tendency to depart from the β2-structure toward the one less demanding in terms of chemical uniformity of side chains: β1-structure. The varying predisposition to form β1- or β2-type aggregates assessed by infrared absorption was compared with the degree of morphological order observed in electron microscopy images. Our results are discussed in the context of latent covalent defects in homopolypeptides (especially with side chains capable of hydrogen-bonding) that could obscure their actual propensities to adopt different conformations, and limit applications in the field of synthetic biomaterials.
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Affiliation(s)
- Aleksandra Fulara
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Agnieszka Hernik
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Hanna Nieznańska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Dzwolak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
- * E-mail:
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28
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Panek PT, Jacob CR. Efficient calculation of anharmonic vibrational spectra of large molecules with localized modes. Chemphyschem 2014; 15:3365-77. [PMID: 25080397 DOI: 10.1002/cphc.201402251] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 11/11/2022]
Abstract
The analysis and interpretation of the vibrational spectra of complex (bio)molecular systems, such as polypeptides and proteins, requires support from quantum-chemical calculations. Such calculations are currently restricted to the harmonic approximation. Here, we show how one of the main bottlenecks in such calculations, the evaluation of the potential energy surface, can be overcome by using localized modes instead of the commonly employed normal modes. We apply such local vibrational self-consistent field (L-VSCF) and vibrational configuration interaction (L-VCI) calculations to a cyclic water tetramer and a helical hexa-alanine peptide. The results show that the use of localized modes is equivalent to the commonly used normal modes, but offers several advantages. First, a faster convergence with respect to the excitation level is observed in L-VCI calculations. Second, the localized modes provide a reduced representation of the couplings between modes that show a regular coupling pattern. This can be used to disregard a significant number of small two-mode potentials a priori. Several such reduced coupling approximations are explored, and we show that the number of single-point calculations required to evaluate the potential energy surface can be significantly reduced without introducing noticeable errors in the resulting vibrational spectra.
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Affiliation(s)
- Paweł T Panek
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures and Institute of Physical Chemistry, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe (Germany) http://www.christophjacob.eu
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29
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Kessler J, Keiderling TA, Bouř P. Arrangement of Fibril Side Chains Studied by Molecular Dynamics and Simulated Infrared and Vibrational Circular Dichroism Spectra. J Phys Chem B 2014; 118:6937-45. [DOI: 10.1021/jp502178d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Kessler
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 166
10 Prague, Czech Republic
- Department
of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 40 Prague, Czech Republic
| | - Timothy A. Keiderling
- Department
of Chemistry, University of Illinois at Chicago, 845 West Taylor
Street, Chicago, Illinois 60607-7061, United States
| | - Petr Bouř
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo
náměstí 2, 166
10 Prague, Czech Republic
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30
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Moran SD, Zanni MT. How to Get Insight into Amyloid Structure and Formation from Infrared Spectroscopy. J Phys Chem Lett 2014; 5:1984-1993. [PMID: 24932380 PMCID: PMC4051309 DOI: 10.1021/jz500794d] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 05/16/2014] [Indexed: 05/17/2023]
Abstract
There is an enormous amount of interest in the structures and formation mechanisms of amyloid fibers. In this Perspective, we review the most common structural motifs of amyloid fibers and discuss how infrared spectroscopy and isotope labeling can be used to identify their structures and aggregation kinetics. We present three specific strategies, site-specific labeling to obtain residue-by-residue structural information, isotope dilution of uniformly labeled proteins for identifying structural folds and protein mixtures, and expressed protein ligation for studying the domain structures of large proteins. For each of these methods, vibrational couplings are the source of the identifying features in the infrared spectrum. Examples are provided using the proteins hIAPP, Aβ, polyglutamine, and γD-crystallin. We focus on FTIR spectroscopy but also describe new observables made possible by 2D IR spectroscopy.
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31
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Kessler J, Bouř P. Molecular dynamics with helical periodic boundary conditions. J Comput Chem 2014; 35:1552-9. [DOI: 10.1002/jcc.23653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/20/2014] [Accepted: 05/26/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Jiří Kessler
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences; Flemingovo náměstí 2 166 10 Prague Czech Republic
- Department of Physical and Macromolecular Chemistry; Faculty of Science, Charles University; Hlavova 8 128 40 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences; Flemingovo náměstí 2 166 10 Prague Czech Republic
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32
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Zhang G, Keiderling TA. Equilibrium and dynamic spectroscopic studies of the interaction of monomeric β-lactoglobulin with lipid vesicles at low pH. Biochemistry 2014; 53:3079-87. [PMID: 24773452 DOI: 10.1021/bi500027x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
β-Lactoglobulin (βLG) is a member of the lipocalin protein family that changes structure upon interacting with anionic surfactants and lipid vesicles under higher-pH conditions at which βLG is dimeric. In this study, a β-sheet to α-helix transformation was also observed for monomeric βLG obtained at pH 2.6 when it was mixed with small unilamellar vesicles (SUVs) of zwitterionic lipids, but being mixed with anionic lipids produced little change. The dynamics and extent of this change were quite dependent on the lipid character, phase, and vesicle size. With 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), at ~50 °C and pH 2.6, the βLG converted to a substantially helical form upon addition of ~10 mM lipid in a two-step kinetic process having time constants of ~1 and ~25 h, as monitored by circular dichroism (CD). Fluorescence changes were simpler but implied a rapid initial change in the Trp environments followed by a slower process paralleling the change in secondary structure. Polarization attenuated total reflectance Fourier transform infrared results indicate the formed helices are at least partially inserted into the lipid bilayer and the sheet segments are on the surface. Thermal behavior showed that the secondary structure of the lipid-bound βLG had two phases, the first being characteristic of the protein-lipid vesicle interaction and the second following the DSPC phase change after which the protein apparently dissociated from the vesicle. Large unilamellar vesicles had a weaker interaction, as judged by CD, which may correlate to the partial exposure of the hydrophobic parts of the SUV bilayer. Other zwitterionic lipids bound βLG with much slower kinetics and often required sonication to induce interaction, but these also showed dissociation upon lipid phase change. These thermal and kinetic behaviors suggest a mechanism for the interaction of monomeric βLG with zwitterionic lipids different from that seen previously for the dimeric form.
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Affiliation(s)
- Ge Zhang
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street (m/c 111), Chicago, Illinois 60607-7061, United States
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33
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Dzwolak W. Chirality and Chiroptical Properties of Amyloid Fibrils. Chirality 2014; 26:580-7. [DOI: 10.1002/chir.22335] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/28/2014] [Indexed: 01/23/2023]
Affiliation(s)
- Wojciech Dzwolak
- Biological and Chemical Research Centre, Department of Chemistry; University of Warsaw; Warsaw Poland
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Kubelka GS, Kubelka J. Site-Specific Thermodynamic Stability and Unfolding of a de Novo Designed Protein Structural Motif Mapped by 13C Isotopically Edited IR Spectroscopy. J Am Chem Soc 2014; 136:6037-48. [DOI: 10.1021/ja500918k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ginka S. Kubelka
- Department
of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Jan Kubelka
- Department
of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
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