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Martínez-Parra JM, Gómez-Ojea R, Daudey GA, Calvelo M, Fernández-Caro H, Montenegro J, Bergueiro J. Exo-chirality of the α-helix. Nat Commun 2024; 15:6987. [PMID: 39143054 PMCID: PMC11325010 DOI: 10.1038/s41467-024-51072-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 07/30/2024] [Indexed: 08/16/2024] Open
Abstract
The structure of helical polymers is dictated by the molecular chirality of their monomer units. Particularly, macromolecular helices with monomer sequence control have the potential to generate chiral topologies. In α-helical folded peptides, the sequential repetition of amino acids generates a chiral layer defined by the amino acid side chains projected outside the amide backbone. Despite being closely related to peptides' structural and functional properties, to the best of our knowledge, a general exo-helical symmetry model has not been yet described for the α-helix. Here, we perform the theoretical, computational, and spectroscopic elucidation of the α-helix principal exo-helical topologies. Non-canonical labeled amino acids are employed to spectroscopically characterize the different exo-helical topologies in solution, which precisely match the theorical prediction. Backbone-to-chromophore distance also shows the expected impact in the exo-helices' geometry and spectroscopic fingerprint. Theoretical prediction and spectroscopic validation of this exo-helical topological model provides robust experimental evidence of the chiral potential on the surface of helical peptides and outlines an entirely new structural scenario for the α-helix.
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Affiliation(s)
- Jose M Martínez-Parra
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Rebeca Gómez-Ojea
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Geert A Daudey
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Martin Calvelo
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Hector Fernández-Caro
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Javier Montenegro
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain.
| | - Julian Bergueiro
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain.
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2
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Wang X, Greenblatt HM, Bigman LS, Yu B, Pletka CC, Levy Y, Iwahara J. Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions. J Mol Biol 2021; 433:167122. [PMID: 34181980 DOI: 10.1016/j.jmb.2021.167122] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/03/2021] [Accepted: 06/22/2021] [Indexed: 10/21/2022]
Abstract
Highly negatively charged segments containing only aspartate or glutamate residues ("D/E repeats") are found in many eukaryotic proteins. For example, the C-terminal 30 residues of the HMGB1 protein are entirely D/E repeats. Using nuclear magnetic resonance (NMR), fluorescence, and computational approaches, we investigated how the D/E repeats causes the autoinhibition of HMGB1 against its specific binding to cisplatin-modified DNA. By varying ionic strength in a wide range (40-900 mM), we were able to shift the conformational equilibrium between the autoinhibited and uninhibited states toward either of them to the full extent. This allowed us to determine the macroscopic and microscopic equilibrium constants for the HMGB1 autoinhibition at various ionic strengths. At a macroscopic level, a model involving the autoinhibited and uninhibited states can explain the salt concentration-dependent binding affinity data. Our data at a microscopic level show that the D/E repeats and other parts of HMGB1 undergo electrostatic fuzzy interactions, each of which is weaker than expected from the macroscopic autoinhibitory effect. This discrepancy suggests that the multivalent nature of the fuzzy interactions enables strong autoinhibition at a macroscopic level despite the relatively weak intramolecular interaction at each site. Both experimental and computational data suggest that the D/E repeats interact preferentially with other intrinsically disordered regions (IDRs) of HMGB1. We also found that mutations mimicking post-translational modifications relevant to nuclear export of HMGB1 can moderately modulate DNA-binding affinity, possibly by impacting the autoinhibition. This study illuminates a functional role of the fuzzy interactions of D/E repeats.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Channing C Pletka
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA.
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3
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Shimato T, Kasahara K, Higo J, Takahashi T. Effects of number of parallel runs and frequency of bias-strength replacement in generalized ensemble molecular dynamics simulations. PEERJ PHYSICAL CHEMISTRY 2019. [DOI: 10.7717/peerj-pchem.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background
The generalized ensemble approach with the molecular dynamics (MD) method has been widely utilized. This approach usually has two features. (i) A bias potential, whose strength is replaced during a simulation, is applied. (ii) Sampling can be performed by many parallel runs of simulations. Although the frequency of the bias-strength replacement and the number of parallel runs can be adjusted, the effects of these settings on the resultant ensemble remain unclear.
Method
In this study, we performed multicanonical MD simulations for a foldable mini-protein (Trp-cage) and two unstructured peptides (8- and 20-residue poly-glutamic acids) with various settings.
Results
As a result, running many short simulations yielded robust results for the Trp-cage model. Regarding the frequency of the bias-potential replacement, although using a high frequency enhanced the traversals in the potential energy space, it did not promote conformational changes in all the systems.
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Affiliation(s)
- Takuya Shimato
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Hyogo, Japan
| | - Takuya Takahashi
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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4
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Nishigami H, Kang J, Terada RI, Kino H, Yamasaki K, Tateno M. Is it possible for short peptide composed of positively- and negatively-charged "hydrophilic" amino acid residue-clusters to form metastable "hydrophobic" packing? Phys Chem Chem Phys 2019; 21:9683-9693. [PMID: 30829349 DOI: 10.1039/c9cp00103d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We theoretically and experimentally analyzed a conformational ensemble of a small, characteristic polypeptide consisting of positively- and negatively-charged amino acid residue clusters, (Lys)9(Glu)9(Lys)9, designed based on the supercoiled DNA-recognition (SDR) domain, with the capability of preferentially binding to supercoiled DNA. Advanced molecular dynamics (MD) simulations coupled with a generalized ensemble technique revealed that substantial amounts of ordered, helical structures were present at the boundaries of the Lys and Glu segments in the obtained conformational ensemble. In fact, the helical content of the peptide calculated from our MD simulations was consistent with that estimated from our experimental analysis employing circular dichroism (CD) spectroscopy. The statistical analysis of the structural ensemble revealed the metastable hydrophobic contact clusters, which were stabilized by closely cohesive residue contacts, formed through "hybrid" hydrophobic (methylene groups) and electrostatic (salt bridges) residue contacts. Both short-range and long-range residue contacts were involved in the metastable hydrophobic clusters, constituting the aforementioned local helical conformations and the compact entire structures, respectively. A significant helical propensity was also found in the (Lys)n and (Glu)m boundaries of other conventional protein structures deposited in the Protein Data Bank (PDB), thus indicating the generality of this conformational trend that has been identified herein.
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Affiliation(s)
- Hiroshi Nishigami
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Hyogo 678-1297, Japan.
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Mariño L, Casasnovas R, Ramis R, Vilanova B, Ortega-Castro J, Frau J, Adrover M. Does glycation really distort the peptide α-helicity? Int J Biol Macromol 2019; 129:254-266. [DOI: 10.1016/j.ijbiomac.2019.01.213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/23/2018] [Accepted: 01/31/2019] [Indexed: 01/19/2023]
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6
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Abraham B, Henning R, Kosheleva I, Chen LX. Revealing Fast Structural Dynamics in pH-Responsive Peptides with Time-Resolved X-ray Scattering. J Phys Chem B 2019; 123:2016-2021. [PMID: 30763085 PMCID: PMC6533112 DOI: 10.1021/acs.jpcb.9b00072] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Many biomaterials can adapt to changes in the local biological environment (such as pH, temperature, or ionic composition) in order to regulate function or deliver a payload. Such adaptation to environmental perturbation is typically a hierarchical process that begins with a response at a local structural level and then propagates to supramolecular and macromolecular scales. Understanding fast structural dynamics that occur upon perturbation is important for rational design of functional biomaterials. However, few nanosecond time-resolved methods can probe both intra- and intermolecular scales simultaneously with a high structural resolution. Here, we utilize time-resolved X-ray scattering to probe nanosecond to microsecond structural dynamics of poly-l-glutamic acid undergoing protonation via a pH jump initiated by photoexcitation of a photoacid. Our results provide insights into the protonation-induced hierarchical changes in packing of peptide chains, formation of a helical structure, and the associated collapse of the peptide chain.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Denis Leshchev
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Darren J. Hsu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Jiyun Hong
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Baxter Abraham
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lin X. Chen
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
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7
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Ogasawara N, Kasahara K, Iwai R, Takahashi T. Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations. PeerJ 2018; 6:e4769. [PMID: 29780670 PMCID: PMC5958886 DOI: 10.7717/peerj.4769] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/24/2018] [Indexed: 11/20/2022] Open
Abstract
Elucidating the molecular mechanism of helix-coil transitions of short peptides is a long-standing conundrum in physical chemistry. Although the helix-coil transitions of poly-glutamic acid (PGA) have been extensively studied, the molecular details of its unfolding process still remain unclear. We performed all-atom canonical molecular dynamics simulations for a 20-residue PGA, over a total of 19 μs, in order to investigate its helix-unfolding processes in atomic resolution. Among the 28 simulations, starting with the α-helical conformation, all showed an unfolding process triggered by the unwinding of terminal residues, rather than by kinking and unwinding of the middle region of the chain. The helix-coil-helix conformation which is speculated by the previous experiments was not observed. Upon comparison between the N- and C-termini, the latter tended to be unstable and easily unfolded. While the probabilities of helix elongation were almost the same among the N-terminal, middle, and C-terminal regions of the chain, unwinding of the helix was enriched at the C-terminal region. The turn and 310-helix conformations were kinetic intermediates in the formation and deformation of α-helix, consistent with the previous computational studies for Ala-based peptides.
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Affiliation(s)
- Naoki Ogasawara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Ryosuke Iwai
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takuya Takahashi
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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8
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Salamatova E, Cunha AV, Bloem R, Roeters SJ, Woutersen S, Jansen TLC, Pshenichnikov MS. Hydrophobic Collapse in N-Methylacetamide-Water Mixtures. J Phys Chem A 2018; 122:2468-2478. [PMID: 29425450 PMCID: PMC6028151 DOI: 10.1021/acs.jpca.8b00276] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/02/2018] [Indexed: 11/28/2022]
Abstract
Aqueous N-methylacetamide solutions were investigated by polarization-resolved pump-probe and 2D infrared spectroscopy (2D IR), using the amide I mode as a reporter. The 2D IR results are compared with molecular dynamics simulations and spectral calculations to gain insight into the molecular structures in the mixture. N-Methylacetamide and water molecules tend to form clusters with "frozen" amide I dynamics. This is driven by a hydrophobic collapse as the methyl groups of the N-methylacetamide molecules cluster in the presence of water. Since the studied system can be considered as a simplified model for the backbone of proteins, the present study forms a convenient basis for understanding the structural and vibrational dynamics in proteins. It is particularly interesting to find out that a hydrophobic collapse as the one driving protein folding is observed in such a simple system.
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Affiliation(s)
- Evgeniia Salamatova
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V. Cunha
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robbert Bloem
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Steven J. Roeters
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maxim S. Pshenichnikov
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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9
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Batys P, Luukkonen S, Sammalkorpi M. Ability of the Poisson-Boltzmann equation to capture molecular dynamics predicted ion distribution around polyelectrolytes. Phys Chem Chem Phys 2018; 19:24583-24593. [PMID: 28853454 DOI: 10.1039/c7cp02547e] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here, we examine polyelectrolyte (PE) and ion chemistry specificity in ion condensation via all-atom molecular dynamics (MD) simulations and assess the ability of the Poisson-Boltzmann (PB) equation to describe the ion distribution predicted by the MD simulations. The PB model enables the extraction of parameters characterizing ion condensation. We find that the modified PB equation which contains the effective PE radius and the energy of the ion-specific interaction as empirical fitting parameters describes ion distribution accurately at large distances but close to the PE, especially when strongly localized charge or specific ion binding sites are present, the mean field description of PB fails. However, the PB model captures the MD predicted ion condensation in terms of the Manning radius and fraction of condensed counterions for all the examined PEs and ion species. We show that the condensed ion layer thickness in our MD simulations collapses on a single master curve for all the examined simple, monovalent ions (Na+, Br+, Cs+, Cl-, and Br-) and PEs when plotted against the Manning parameter (and consequently the PE line charge density). The significance of this finding is that, contrary to the Manning radius extracted from the mean field PB model, the condensed layer thickness in the all atom detail MD modelling does not depend on the PE chemistry or counterion type. Furthermore, the fraction of condensed counterions in the MD simulations exceeds the PB theory prediction. The findings contribute toward understanding and modelling ion distribution around PEs and other charged macromolecules in aqueous solutions, such as DNA, functionalized nanotubes, and viruses.
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Affiliation(s)
- Piotr Batys
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
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10
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Popp A, Scheerer D, Heck B, Hauser K. Biomolecular dynamics studied with IR-spectroscopy using quantum cascade lasers combined with nanosecond perturbation techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:192-199. [PMID: 28364666 DOI: 10.1016/j.saa.2017.03.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/17/2017] [Accepted: 03/19/2017] [Indexed: 06/07/2023]
Abstract
Early events of protein folding can be studied with fast perturbation techniques triggering non-equilibrium relaxation dynamics. A nanosecond laser-excited pH-jump or temperature-jump (T-jump) was applied to initiate helix folding or unfolding of poly-l-glutamic acid (PGA). PGA is a homopolypeptide with titratable carboxyl side-chains whose protonation degree determines the PGA conformation. A pH-jump was realized by the photochemical release of protons and induces PGA folding due to protonation of the side-chains. Otherwise, the helical conformation can be unfolded by a T-jump. We operated under conditions where PGA does not aggregate and temperature and pH are the regulatory properties of its conformation. The experiments were performed in such a manner that the folding/unfolding jump proceeded to the same PGA conformation. We quantified the increase/decrease in helicity induced by the pH-/T-jump and demonstrated that the T-jump results in a relatively small change in helical content in contrast to the pH-jump. This is caused by the strong pH-dependence of the PGA conformation. The conformational changes were detected by time-resolved single wavelength IR-spectroscopy using quantum cascade lasers (QCL). We could independently observe the kinetics for α-helix folding and unfolding in PGA by using different perturbation techniques and demonstrate the high sensitivity of time-resolved IR-spectroscopy to study protein folding mechanisms.
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Affiliation(s)
- Alexander Popp
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - David Scheerer
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Benjamin Heck
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.
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11
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Dubey P, Murab S, Karmakar S, Chowdhury PK, Ghosh S. Modulation of Self-Assembly Process of Fibroin: An Insight for Regulating the Conformation of Silk Biomaterials. Biomacromolecules 2015; 16:3936-44. [PMID: 26575529 DOI: 10.1021/acs.biomac.5b01258] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Controlling the mechanism of self-assembly in proteins has emerged as a potent tool for various biomedical applications. Silk fibroin self-assembly consists of gradual conformational transition from random coil to β-sheet structure. In this work we elucidated the intermediate secondary conformation in the presence of Ca(2+) ions during fibroin self-assembly. The interaction of fibroin and calcium ions resulted in a predominantly α-helical intermediate conformation, which was maintained to certain extent even in the final conformation as illustrated by circular dichroism and attenuated total reflectance-Fourier transform infrared spectroscopy. Further, to elucidate the mechanism behind this interaction molecular modeling of the N-terminal region of fibroin with Ca(2+) ions was performed. Negatively charged glutamate and aspartate amino acids play a key role in the electrostatic interaction with positively charged calcium ions. Therefore, insights about modulation of self-assembly mechanism of fibroin could potentially be utilized to develop silk-based biomaterials consisting of the desired secondary conformation.
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Affiliation(s)
- Priyanka Dubey
- Department of Textile Technology and ‡Department of Chemistry, Indian Institute of Technology Delhi , Hauz Khas, New Delhi 110016, India
| | - Sumit Murab
- Department of Textile Technology and ‡Department of Chemistry, Indian Institute of Technology Delhi , Hauz Khas, New Delhi 110016, India
| | - Sandip Karmakar
- Department of Textile Technology and ‡Department of Chemistry, Indian Institute of Technology Delhi , Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Textile Technology and ‡Department of Chemistry, Indian Institute of Technology Delhi , Hauz Khas, New Delhi 110016, India
| | - Sourabh Ghosh
- Department of Textile Technology and ‡Department of Chemistry, Indian Institute of Technology Delhi , Hauz Khas, New Delhi 110016, India
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12
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Crisostomo AC, Dang L, Digambaranath JL, Klaver AC, Loeffler DA, Payne JJ, Smith LM, Yokom AL, Finke JM. Biophysical characterization data on Aβ soluble oligomers produced through a method enabling prolonged oligomer stability and biological buffer conditions. Data Brief 2015; 4:650-8. [PMID: 26401521 PMCID: PMC4560727 DOI: 10.1016/j.dib.2015.07.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/28/2015] [Accepted: 07/28/2015] [Indexed: 11/29/2022] Open
Abstract
The data here consists of time-dependent experimental parameters from chemical and biophysical methods used to characterize Aβ monomeric reactants as well as soluble oligomer and amyloid fibril products from a slow (3–4 week) assembly reaction under biologically-relevant solvent conditions. The data of this reaction are both of a qualitative and quantitative nature, including gel images from chemical cross-linking and Western blots, fractional solubility, thioflavin T binding, size exclusion chromatograms, transmission electron microscopy images, circular dichroism spectra, and fluorescence resonance energy transfer efficiencies of donor–acceptor pair labels in the Aβ chain. This data enables future efforts to produce the initial monomer and eventual soluble oligomer and amyloid fibril states by providing reference benchmarks of these states pertaining to physical properties (solubility), ligand-binding (thioflavin T binding), mesoscopic structure (electron microscopy, size exclusion chromatography, cross-linking products, SDS and native gels) and molecular structure (circular dichroism, FRET donor-acceptor distance). Aβ1-40 soluble oligomers are produced that are suitable for biophysical studies requiring sufficient transient stability to exist in their “native” conformation in biological phosphate-saline buffers for extended periods of time. The production involves an initial preparation of highly monomeric Aβ in a phosphate saline buffer that transitions to fibrils and oligomers through time incubation alone, without added detergents or non-aqueous chemicals. This criteria ensures that the only difference between initial monomeric Aβ reactant and subsequent Aβ oligomer products is their degree of peptide assembly. A number of chemical and biophysical methods were used to characterize the monomeric reactants and soluble oligomer and amyloid fibril products, including chemical cross-linking, Western blots, fraction solubility, thioflvain T binding, size exclusion chromatography, transmission electron micrscopy, circular dichroism spectroscopy, and fluorescence resonance energy transfer.
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Affiliation(s)
- Amanda C Crisostomo
- Sciences and Mathematics, IAS, University of Washington, Tacoma, WA 98402, United States
| | - Loan Dang
- Eye Research Institute, Oakland University, Rochester, MI 48309, United States
| | | | - Andrea C Klaver
- Department of Neurology Research, Beaumont Health System, Royal Oak MI, United States
| | - David A Loeffler
- Department of Neurology Research, Beaumont Health System, Royal Oak MI, United States
| | - Jeremiah J Payne
- Sciences and Mathematics, IAS, University of Washington, Tacoma, WA 98402, United States
| | - Lynnae M Smith
- Department of Neurology Research, Beaumont Health System, Royal Oak MI, United States
| | - Adam L Yokom
- Department of Chemistry, Oakland University, Rochester MI 48309, United States
| | - John M Finke
- Sciences and Mathematics, IAS, University of Washington, Tacoma, WA 98402, United States
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13
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14
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Gregory MJ, Anderson M, Causgrove TP. Measurement of energy barriers to conformational change in poly-l-glutamic acid by temperature-derivative spectroscopy. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Lampi MC, Wu X, Schilke KF, McGuire J. Structural attributes affecting peptide entrapment in PEO brush layers. Colloids Surf B Biointerfaces 2013; 106:79-85. [PMID: 23434695 DOI: 10.1016/j.colsurfb.2013.01.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 01/17/2013] [Accepted: 01/18/2013] [Indexed: 11/28/2022]
Abstract
A more quantitative understanding of peptide loading and release from polyethylene oxide (PEO) brush layers will provide direction for development of new strategies for drug storage and delivery. In this work we recorded selected effects of peptide structure and amphiphilicity on adsorption into PEO brush layers based on covalently stabilized Pluronic(®)F 108. Optical waveguide lightmode spectroscopy and circular dichroism measurements were used to characterize the adsorption of poly-l-glutamic acid, poly-l-lysine, and the cationic amphiphilic peptide WLBU2, to the brush layers. The structure of WLBU2 as well as that of the similarly-sized homopolymers was controlled between disordered and more ordered (helical) forms by varying solution conditions. Adsorption kinetic patterns were interpreted with reference to a simple model for protein adsorption, in order to evaluate rate constants for peptide adsorption and desorption from loosely and tightly bound states. While more ordered peptide structure apparently promoted faster adsorption and elution rates, resistance to elution while in the PEO layer was dependent on peptide amphiphilicity. The results presented here are compelling evidence of the potential to create anti-fouling surface coatings capable of storing and delivering therapeutics.
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Affiliation(s)
- Marsha C Lampi
- School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
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16
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Digambaranath JL, Campbell TV, Chung A, McPhail MJ, Stevenson KE, Zohdy MA, Finke JM. An accurate model of polyglutamine. Proteins 2011; 79:1427-40. [DOI: 10.1002/prot.22970] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 11/15/2010] [Accepted: 12/08/2010] [Indexed: 01/15/2023]
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17
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Dzubiella J. Molecular Insights into the Ion-Specific Kinetics of Anionic Peptides. J Phys Chem B 2010; 114:7098-103. [DOI: 10.1021/jp1010814] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Joachim Dzubiella
- Physics Department T37, Technical University Munich, 85748 Garching, Germany
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18
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Lignell M, Tegler LT, Becker HC. Hydrated and dehydrated tertiary interactions--opening and closing--of a four-helix bundle peptide. Biophys J 2009; 97:572-80. [PMID: 19619472 DOI: 10.1016/j.bpj.2009.04.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 03/26/2009] [Accepted: 04/01/2009] [Indexed: 11/15/2022] Open
Abstract
The structural heterogeneity and thermal denaturation of a dansyl-labeled four-helix bundle homodimeric peptide was studied with steady-state and time-resolved fluorescence spectroscopy and with circular dichroism (CD). At room temperature the fluorescence decay of the polarity-sensitive dansyl, located in the hydrophobic core region, can be described by a broad distribution of fluorescence lifetimes, reflecting the heterogeneous microenvironment. However, the lifetime distribution is nearly bimodal, which we ascribe to the presence of two major conformational subgroups. Since the fluorescence lifetime reflects the water content of the four-helix bundle conformations, we can use the lifetime analysis to monitor the change in hydration state of the hydrophobic core of the four-helix bundle. Increasing the temperature from 9 degrees C to 23 degrees C leads to an increased population of molten-globule-like conformations with a less ordered helical backbone structure. The fluorescence emission maximum remains constant in this temperature interval, and the hydrophobic core is not strongly affected. Above 30 degrees C the structural dynamics involve transient openings of the four-helix bundle structure, as evidenced by the emergence of a water-quenched component and less negative CD. Above 60 degrees C the homodimer starts to dissociate, as shown by the increasing loss of CD and narrow, short-lived fluorescence lifetime distributions.
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Affiliation(s)
- Martin Lignell
- Department of Photochemistry and Molecular Sciences, Uppsala University, Uppsala, Sweden
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19
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Kumar R, Bhuyan AK. Viscosity scaling for the glassy phase of protein folding. J Phys Chem B 2008; 112:12549-54. [PMID: 18781712 DOI: 10.1021/jp804021d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although commendable progress has been made in the understanding of the physics of protein folding, a key unresolved issue is whether Kramers' diffusion model of chemical reactions is generally applicable to activated barrier crossing events during folding. To examine the solvent viscosity effect on the folding transition of native-like trapped intermediates, laser flash photolysis has been used to measure the microsecond folding kinetics of a natively folded state of CO-liganded ferrocytochrome c (M-state) in the 1-250 cP range of glycerol viscosity at pH 7.0, 20 degrees C. The single rate coefficient for the folding of the M-state to the native state of the protein (i.e., the M --> N folding process) decreases initially when the solvent viscosity is low (<10 cP), but saturates at higher viscosity, indicating that Kramers model is not general enough for scaling the viscosity dependence of post-transition folding involving glassy dynamics. Analysis based on the Grote-Hynes idea of time dependent friction in conjunction with defect diffusion dynamics can account for the observed non-Kramers scaling.
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Affiliation(s)
- Rajesh Kumar
- Schools of Chemistry and Life Sciences, University of Hyderabad, Hyderabad, India
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Ackbarow T, Chen X, Keten S, Buehler MJ. Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains. Proc Natl Acad Sci U S A 2007; 104:16410-5. [PMID: 17925444 PMCID: PMC2034213 DOI: 10.1073/pnas.0705759104] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Indexed: 11/18/2022] Open
Abstract
The fundamental fracture mechanisms of biological protein materials remain largely unknown, in part, because of a lack of understanding of how individual protein building blocks respond to mechanical load. For instance, it remains controversial whether the free energy landscape of the unfolding behavior of proteins consists of multiple, discrete transition states or the location of the transition state changes continuously with the pulling velocity. This lack in understanding has thus far prevented us from developing predictive strength models of protein materials. Here, we report direct atomistic simulation that over four orders of magnitude in time scales of the unfolding behavior of alpha-helical (AH) and beta-sheet (BS) domains, the key building blocks of hair, hoof, and wool as well as spider silk, amyloids, and titin. We find that two discrete transition states corresponding to two fracture mechanisms exist. Whereas the unfolding mechanism at fast pulling rates is sequential rupture of individual hydrogen bonds (HBs), unfolding at slow pulling rates proceeds by simultaneous rupture of several HBs. We derive the hierarchical Bell model, a theory that explicitly considers the hierarchical architecture of proteins, providing a rigorous structure-property relationship. We exemplify our model in a study of AHs, and show that 3-4 parallel HBs per turn are favorable in light of the protein's mechanical and thermodynamical stability, in agreement with experimental findings that AHs feature 3.6 HBs per turn. Our results provide evidence that the molecular structure of AHs maximizes its robustness at minimal use of building materials.
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Affiliation(s)
- Theodor Ackbarow
- *Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and
| | - Xuefeng Chen
- *Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Sinan Keten
- *Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and
| | - Markus J. Buehler
- *Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and
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