1
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Li JY, Zhou CM, Jin RL, Song JH, Yang KC, Li SL, Tan BH, Li YC. The detection methods currently available for protein aggregation in neurological diseases. J Chem Neuroanat 2024; 138:102420. [PMID: 38626816 DOI: 10.1016/j.jchemneu.2024.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024]
Abstract
Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.
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Affiliation(s)
- Jing-Yi Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Cheng-Mei Zhou
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Rui-Lin Jin
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Jia-Hui Song
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Ke-Chao Yang
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Shu-Lei Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Bai-Hong Tan
- Laboratory Teaching Center of Basic Medicine, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Yan-Chao Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China.
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2
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Liu B, Fang R, Li W, Wu X, Liu T, Lin M, Sun J, Chen X. Fast Catalyst-Free Synthesis of Stereoselective Polypeptides via Hierarchical Chiral Assembly. J Am Chem Soc 2024. [PMID: 38858162 DOI: 10.1021/jacs.4c03281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Understanding how life's essential homochiral biopolymers arose from racemic precursors is a challenging quest. Herein, we present a groundbreaking approach involving hierarchical chiral assembly-driven stereoselective ring-opening polymerization of ε-benzyloxycarbonyl-l/d-lysine N-carboxyanhydrides assisted by ultrasonication in an aqueous medium. This method enabled a narrow dispersity within a few minutes and the achievement of high molecular weight for polypeptides, employing a living polymerization mechanism. The polymerization of l and d enantiomers yielded predominantly right- and left-handed superhelical assemblies in a one-pot preparation, respectively. Notably, stereoselective polypeptide segments were efficiently prepared through hierarchical assembly-driven polymerization of racemic monomers in the absence of a catalyst. This research offers an innovative strategy for the convenient preparations of stereoenriched polypeptides and, more importantly, sheds light on the plausible emergence of homochiral peptides in the origin of life.
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Affiliation(s)
- Borui Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Rui Fang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Wenlong Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Xiaoyu Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Tianli Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Min Lin
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Jing Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
| | - Xuesi Chen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 130012 Changchun, China
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China
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3
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Abstract
While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Armin Solemanifar
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
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4
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Zhytniakivska O, Kurutos A, Shchuka M, Vus K, Tarabara U, Trusova V, Gorbenko G. Fӧrster resonance energy transfer between Thioflavin T and unsymmetrical trimethine cyanine dyes on amyloid fibril scaffold. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Wang F, Gnewou O, Wang S, Osinski T, Zuo X, Egelman EH, Conticello VP. Deterministic chaos in the self-assembly of β sheet nanotubes from an amphipathic oligopeptide. MATTER 2021; 4:3217-3231. [PMID: 34632372 PMCID: PMC8494133 DOI: 10.1016/j.matt.2021.06.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The self-assembly of designed peptides into filaments and other higher-order structures has been the focus of intense interest because of the potential for creating new biomaterials and biomedical devices. These peptide assemblies have also been used as models for understanding biological processes, such as the pathological formation of amyloid. We investigate the assembly of an octapeptide sequence, Ac-FKFEFKFE-NH2, motivated by prior studies that demonstrated that this amphipathic β strand peptide self-assembled into fibrils and biocompatible hydrogels. Using high-resolution cryoelectron microscopy (cryo-EM), we are able to determine the atomic structure for two different coexisting forms of the fibrils, containing four and five β sandwich protofilaments, respectively. Surprisingly, the inner walls in both forms are parallel β sheets, while the outer walls are antiparallel β sheets. Our results demonstrate the chaotic nature of peptide self-assembly and illustrate the importance of cryo-EM structural analysis to understand the complex phase behavior of these materials at near-atomic resolution.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: (E.H.E.), (V.P.C.)
| | - Vincent P. Conticello
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA 30322, USA
- Lead contact
- Correspondence: (E.H.E.), (V.P.C.)
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Argudo PG, Giner-Casares JJ. Folding and self-assembly of short intrinsically disordered peptides and protein regions. NANOSCALE ADVANCES 2021; 3:1789-1812. [PMID: 36133101 PMCID: PMC9417027 DOI: 10.1039/d0na00941e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/17/2021] [Indexed: 05/15/2023]
Abstract
Proteins and peptide fragments are highly relevant building blocks in self-assembly for nanostructures with plenty of applications. Intrinsically disordered proteins (IDPs) and protein regions (IDRs) are defined by the absence of a well-defined secondary structure, yet IDPs/IDRs show a significant biological activity. Experimental techniques and computational modelling procedures for the characterization of IDPs/IDRs are discussed. Directed self-assembly of IDPs/IDRs allows reaching a large variety of nanostructures. Hybrid materials based on the derivatives of IDPs/IDRs show a promising performance as alternative biocides and nanodrugs. Cell mimicking, in vivo compartmentalization, and bone regeneration are demonstrated for IDPs/IDRs in biotechnological applications. The exciting possibilities of IDPs/IDRs in nanotechnology with relevant biological applications are shown.
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Affiliation(s)
- Pablo G Argudo
- Université de Bordeaux, CNRS, Bordeaux INP, LCPO 16 Avenue Pey-Berland 33600 Pessac France
| | - Juan J Giner-Casares
- Departamento de Química Física y T. Aplicada, Instituto Universitario de Nanoquímica IUNAN, Facultad de Ciencias, Universidad de Córdoba (UCO) Campus de Rabanales, Ed. Marie Curie E-14071 Córdoba Spain
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7
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Polymorphic Aβ42 fibrils adopt similar secondary structure but differ in cross-strand side chain stacking interactions within the same β-sheet. Sci Rep 2020; 10:5720. [PMID: 32235842 PMCID: PMC7109039 DOI: 10.1038/s41598-020-62181-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 03/10/2020] [Indexed: 12/20/2022] Open
Abstract
Formation of polymorphic amyloid fibrils is a common feature in neurodegenerative diseases involving protein aggregation. In Alzheimer’s disease, different fibril structures may be associated with different clinical sub-types. Structural basis of fibril polymorphism is thus important for understanding the role of amyloid fibrils in the pathogenesis and progression of these diseases. Here we studied two types of Aβ42 fibrils prepared under quiescent and agitated conditions. Quiescent Aβ42 fibrils adopt a long and twisted morphology, while agitated fibrils are short and straight, forming large bundles via lateral association. EPR studies of these two types of Aβ42 fibrils show that the secondary structure is similar in both fibril polymorphs. At the same time, agitated Aβ42 fibrils show stronger interactions between spin labels across the full range of the Aβ42 sequence, suggesting a more tightly packed structure. Our data suggest that cross-strand side chain packing interactions within the same β-sheet may play a critical role in the formation of polymorphic fibrils.
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8
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Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
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9
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Gorbenko G, Trusova V, Deligeorgiev T, Gadjev N, Mizuguchi C, Saito H. Two-step FRET as a tool for probing the amyloid state of proteins. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Cieplak AS. Tau Inclusions in Alzheimer's, Chronic Traumatic Encephalopathy and Pick's Disease. A Speculation on How Differences in Backbone Polarization Underlie Divergent Pathways of Tau Aggregation. Front Neurosci 2019; 13:488. [PMID: 31156372 PMCID: PMC6530265 DOI: 10.3389/fnins.2019.00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022] Open
Abstract
Tau-related dementias appear to involve specific to each disease aggregation pathways and morphologies of filamentous tau assemblies. To understand etiology of these differences, here we elucidate molecular mechanism of formation of tau PHFs based on the PMO theory of misfolding and aggregation of pleiomorphic proteins associated with neurodegenerative diseases. In this model, fibrillization of tau is initiated by the coupled binding and folding of the MTB domains that yields antiparallel homodimers, in analogy to folding of split inteins. The free energy of binding is minimized when the antiparallel alignment brings about backbone-backbone H-bonding between the MTBD segments of similar "strand" propensities. To assess these propensities, a function of the NMR shielding tensors of the Cα atoms is introduced as the folding potential function FP i ; the Cα tensors are obtained by the quantum mechanical modeling of protein secondary structure (GIAO//B3LYP/D95**). The calculated FP i plots show that the "strand" propensities of the MBTD segments, and hence the homodimer's register, can be affected by the relatively small changes in the environment's pH, as a result of protonation of MBTD's conserved histidines. The assembly of the antiparallel tau dimers into granular aggregates and their subsequent conversion into the parallel cross-β structure of paired helical filaments is expected to follow the same path as the previously described fibrillization of Aβ. Consequently, the core structure of the nascent tau fibril is determined by the register of the tau homodimer. This model accounts for the reported differences in (i) fibril-core structure of in vivo and in vitro filaments, (ii) cross-seeding of isoforms, (iii) effects of reducing/non-reducing conditions, (iv) effects of PHF6 mutations, and (v) homologs' aggregation properties. The proposed model also suggests that in contrast to Alzheimer's and chronic traumatic encephalopathy disease, the assembly of tau prions in Pick's disease would be facilitated by a moderate drop in pH that accompanies e.g., transit in the endosomal system, inflammation response or an ischemic injury.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Brandeis University, Waltham, MA, United States
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11
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Abstract
A β-strand is a component of a β-sheet and is an important structural motif in biomolecules. An α-helix has clear helicity, while chirality of a β-strand had been discussed on the basis of molecular twists generated by forming hydrogen bonds in parallel or non-parallel β-sheets. Herein we describe handedness determination of two-fold helicity in a zig-zag β-strand structure. Left- (M) and right-handedness (P) of the two-fold helicity was defined by application of two concepts: tilt-chirality and multi-point approximation. We call the two-fold helicity in a β-strand, whose handedness has been unrecognized and unclarified, as hidden chirality. Such hidden chirality enables us to clarify precise chiral characteristics of biopolymers. It is also noteworthy that characterization of chirality of high dimensional structures like a β-strand and α-helix, referred to as high dimensional chirality (HDC) in the present study, will contribute to elucidation of the possible origins of chirality and homochirality in nature because such HDC originates from not only asymmetric centers but also conformations in a polypeptide chain.
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12
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Kikuchi N, Fujiwara K, Ikeguchi M. β‐Strand twisting/bending in soluble and transmembrane β‐barrel structures. Proteins 2018; 86:1231-1241. [DOI: 10.1002/prot.25576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/05/2018] [Accepted: 06/22/2018] [Indexed: 01/03/2023]
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13
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Clarke DE, Parmenter CDJ, Scherman OA. Tunable Pentapeptide Self-Assembled β-Sheet Hydrogels. Angew Chem Int Ed Engl 2018; 57:7709-7713. [PMID: 29603545 PMCID: PMC6055752 DOI: 10.1002/anie.201801001] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Indexed: 01/13/2023]
Abstract
Oligopeptide‐based supramolecular hydrogels hold promise in a range of applications. The gelation of these systems is hard to control, with minor alterations in the peptide sequence significantly influencing the self‐assembly process. We explored three pentapeptide sequences with different charge distributions and discovered that they formed robust, pH‐responsive hydrogels. By altering the concentration and charge distribution of the peptide sequence, the stiffness of the hydrogels could be tuned across two orders of magnitude (2–200 kPa). Also, through reassembly of the β‐sheet interactions the hydrogels could self‐heal and they demonstrated shear‐thin behavior. Using spectroscopic and cryo‐imaging techniques, we investigated the relationship between peptide sequence and molecular structure, and how these influence the mechanical properties of the hydrogel. These pentapeptide hydrogels with tunable morphology and mechanical properties have promise in tissue engineering, injectable delivery vectors, and 3D printing applications.
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Affiliation(s)
- David E Clarke
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Christopher D J Parmenter
- Nottingham Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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14
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Clarke DE, Parmenter CDJ, Scherman OA. Tunable Pentapeptide Self-Assembled β-Sheet Hydrogels. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David E. Clarke
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Christopher D. J. Parmenter
- Nottingham Nanoscale and Microscale Research Centre; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Oren A. Scherman
- Melville Laboratory for Polymer Synthesis; Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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15
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Lahiri P, Verma H, Ravikumar A, Chatterjee J. Protein stabilization by tuning the steric restraint at the reverse turn. Chem Sci 2018; 9:4600-4609. [PMID: 29899953 PMCID: PMC5969505 DOI: 10.1039/c7sc05163h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
The incorporation of pseudoallylic strain by N-methylation at the solvent exposed loop in proteins leads to a stark increase in their thermodynamic stability that can be tuned by altering the amino acid composition.
Reverse turns are solvent-exposed motifs in proteins that are crucial in nucleating β-sheets and drive the protein folding. The solvent-exposed nature makes reverse turns more amenable to chemical modifications than α-helices or β-sheets towards modulating the stability of re-engineered proteins. Here, we utilize van der Waals repulsive forces in tuning the steric restraint at the reverse turn. The steric restraint induced upon N-methylation of the i+1–i+2 amide bond at the reverse turn results in well-folded and stable β-sheets in aqueous solution at room temperature. The developed superactive turn inducing motif is tolerant to a wide variety of functional groups present on coded amino acids making the designed turn fully compatible with bioactive loops in proteins. We demonstrate that the steric restraint and the functional groups at the reverse turn act in synergy to modulate the folding of re-engineered β-sheets. Introduction of the turn motifs onto a three-stranded β-sheet protein, Pin 1 WW domain, resulted in various analogs showing a cooperative two-state transition with thermal stability (TM) ranging from 62 °C to 82 °C. Despite modulating the stability of Pin 1 variants by ∼2.8 kcal mol–1 (ΔΔGf), the native fold in all the protein variants was found to be unperturbed. This structural stability is brought about by conformational preorganization at the engineered reverse turn that results in strong intramolecular hydrogen bonds along the three dimensional structure of the protein. Thus, this simple loop engineering strategy via two amino acid substitution provides us a “toolkit” to modulate the stability of β-sheet containing peptides and proteins in aqueous solution that will greatly expand the scope of de novo protein and foldamer design.
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Affiliation(s)
- Priyanka Lahiri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Ashraya Ravikumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
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16
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Periole X, Huber T, Bonito-Oliva A, Aberg KC, van der Wel PCA, Sakmar TP, Marrink SJ. Energetics Underlying Twist Polymorphisms in Amyloid Fibrils. J Phys Chem B 2018; 122:1081-1091. [PMID: 29254334 PMCID: PMC5857390 DOI: 10.1021/acs.jpcb.7b10233] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Amyloid fibrils are highly ordered protein aggregates associated with more than 40 human diseases. The exact conditions under which the fibrils are grown determine many types of reported fibril polymorphism, including different twist patterns. Twist-based polymorphs display unique mechanical properties in vitro, and the relevance of twist polymorphism in amyloid diseases has been suggested. We present transmission electron microscopy images of Aβ42-derived (amyloid β) fibrils, which are associated with Alzheimer's disease, demonstrating the presence of twist variability even within a single long fibril. To better understand the molecular underpinnings of twist polymorphism, we present a structural and thermodynamics analysis of molecular dynamics simulations of the twisting of β-sheet protofilaments of a well-characterized cross-β model: the GNNQQNY peptide from the yeast prion Sup35. The results show that a protofilament model of GNNQQNY is able to adopt twist angles from -11° on the left-hand side to +8° on the right-hand side in response to various external conditions, keeping an unchanged peptide structure. The potential of mean force (PMF) of this cross-β structure upon twisting revealed that only ∼2kBT per peptide are needed to stabilize a straight conformation with respect to the left-handed free-energy minimum. The PMF also shows that the canonical structural core of β-sheets, i.e., the hydrogen-bonded backbone β-strands, favors the straight conformation. However, the concerted effects of the side chains contribute to twisting, which provides a rationale to correlate polypeptide sequence, environmental growth conditions and number of protofilaments in a fibril with twist polymorphisms.
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Affiliation(s)
- Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Alessandra Bonito-Oliva
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Karina C Aberg
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Patrick C A van der Wel
- Department of Structural Biology and Center for Protein Conformational Diseases, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet , 141 57 Huddinge, Sweden
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
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17
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Iyer A, Roeters SJ, Kogan V, Woutersen S, Claessens MMAE, Subramaniam V. C-Terminal Truncated α-Synuclein Fibrils Contain Strongly Twisted β-Sheets. J Am Chem Soc 2017; 139:15392-15400. [PMID: 28968082 PMCID: PMC5668890 DOI: 10.1021/jacs.7b07403] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
C-terminal truncations
of monomeric wild-type alpha-synuclein (henceforth
WT-αS) have been shown to enhance the formation of amyloid aggregates
both in vivo and in vitro and have
been associated with accelerated progression of Parkinson’s
disease (PD). The correlation with PD may not solely be a result of
faster aggregation, but also of which fibril polymorphs are preferentially
formed when the C-terminal residues are deleted. Considering that
different polymorphs are known to result in distinct pathologies,
it is important to understand how these truncations affect the organization
of αS into fibrils. Here we present high-resolution microscopy
and advanced vibrational spectroscopy studies that indicate that the
C-terminal truncation variant of αS, lacking residues 109–140
(henceforth referred to as 1–108-αS), forms amyloid fibrils
with a distinct structure and morphology. The 1–108-αS
fibrils have a unique negative circular dichroism band at ∼230
nm, a feature that differs from the canonical ∼218 nm band
usually observed for amyloid fibrils. We show evidence that 1–108-αS
fibrils consist of strongly twisted β-sheets with an increased
inter-β-sheet distance and a higher solvent exposure than WT-αS
fibrils, which is also indicated by the pronounced differences in
the 1D-IR (FTIR), 2D-IR, and vibrational circular dichroism spectra.
As a result of their distinct β-sheet structure, 1–108-αS
fibrils resist incorporation of WT-αS monomers.
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Affiliation(s)
- Aditya Iyer
- Nanoscale Biophysics Group, AMOLF , Science Park 104, Amsterdam 1098 XG, The Netherlands.,Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands
| | - Steven J Roeters
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Vladimir Kogan
- Dannalab BV , Wethouder Beversstraat 185, Enschede 7543 BK, The Netherlands
| | - Sander Woutersen
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands
| | - Vinod Subramaniam
- Nanoscale Biophysics Group, AMOLF , Science Park 104, Amsterdam 1098 XG, The Netherlands.,Nanobiophysics Group, MESA+ Institute for Nanotechnology, University of Twente , Drienerlolaan 5, Enschede 7522 NB, The Netherlands.,Vrije Universiteit Amsterdam , De Boelelaan 1105, Amsterdam 1081 HV, The Netherlands
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18
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Cieplak AS. Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions. PLoS One 2017; 12:e0180905. [PMID: 28922400 PMCID: PMC5603215 DOI: 10.1371/journal.pone.0180905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the Cα atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrPC, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrPSc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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19
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Samad MB, Chhonker YS, Contreras JI, McCarthy A, McClanahan MM, Murry DJ, Conda-Sheridan M. Developing Polyamine-Based Peptide Amphiphiles with Tunable Morphology and Physicochemical Properties. Macromol Biosci 2017; 17. [DOI: 10.1002/mabi.201700096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/05/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Mehdi Bin Samad
- College of Pharmacy; Department of Pharmaceutical Sciences; University of Nebraska Medical Center; Omaha NE 68198-6125 USA
| | - Yashpal Singh Chhonker
- College of Pharmacy; Department of Pharmacy Practice; University of Nebraska Medical Center; Omaha NE 68198-6145 USA
| | - Jacob I. Contreras
- Eppley Institute for Research in Cancer and Allied Diseases; University of Nebraska Medical Center; Omaha NE 68022 USA
| | - Alec McCarthy
- Department of Biological Systems Engineering; University of Nebraska-Lincoln; Lincoln NE 68588 USA
| | - Megan M. McClanahan
- Division of Natural Science and Mathematics; Chaminade University of Honolulu; Honolulu HI 96816 USA
| | - Daryl J. Murry
- College of Pharmacy; Department of Pharmacy Practice; University of Nebraska Medical Center; Omaha NE 68198-6145 USA
| | - Martin Conda-Sheridan
- College of Pharmacy; Department of Pharmaceutical Sciences; University of Nebraska Medical Center; Omaha NE 68198-6125 USA
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20
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Xiang S, Kulminskaya N, Habenstein B, Biernat J, Tepper K, Paulat M, Griesinger C, Becker S, Lange A, Mandelkow E, Linser R. A Two-Component Adhesive: Tau Fibrils Arise from a Combination of a Well-Defined Motif and Conformationally Flexible Interactions. J Am Chem Soc 2017; 139:2639-2646. [PMID: 28124562 DOI: 10.1021/jacs.6b09619] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fibrillar aggregates of Aβ and Tau in the brain are the major hallmarks of Alzheimer's disease. Most Tau fibers have a twisted appearance, but the twist can be variable and even absent. This ambiguity, which has also been associated with different phenotypes of tauopathies, has led to controversial assumptions about fibril constitution, and it is unclear to-date what the molecular causes of this polymorphism are. To tackle this question, we used solid-state NMR strategies providing assignments of non-seeded three-repeat-domain Tau3RD with an inherent heterogeneity. This is in contrast to the general approach to characterize the most homogeneous preparations by construct truncation or intricate seeding protocols. Here, carbon and nitrogen chemical-shift conservation between fibrils revealed invariable secondary-structure properties, however, with inter-monomer interactions variable among samples. Residues with variable amide shifts are localized mostly to N- and C-terminal regions within the rigid beta structure in the repeat region of Tau3RD. By contrast, the hexapeptide motif in repeat R3, a crucial motif for fibril formation, shows strikingly low variability of all NMR parameters: Starting as a nucleation site for monomer-monomer contacts, this six-residue sequence element also turns into a well-defined structural element upon fibril formation. Given the absence of external causes in vitro, the interplay of structurally differently conserved elements in this protein likely reflects an intrinsic property of Tau fibrils.
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Affiliation(s)
- Shengqi Xiang
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Natalia Kulminskaya
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Birgit Habenstein
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux/CBMN UMR5248 , 2 rue Robert Escarpit, 33600 Pessac, France
| | - Jacek Biernat
- DZNE, German Center for Neurodegenerative Diseases , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,CAESAR Research Center , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Katharina Tepper
- DZNE, German Center for Neurodegenerative Diseases , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,CAESAR Research Center , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Maria Paulat
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Adam Lange
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Institut für Biologie, Humboldt-Universität zu Berlin , Invalidenstrasse 110, 10115 Berlin, Germany.,Department of Molecular Biophysics, Leibniz-Institut für Molekulare Pharmakologie (FMP) , Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Eckhard Mandelkow
- DZNE, German Center for Neurodegenerative Diseases , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,CAESAR Research Center , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,Hamburg Outstation, c/o DESY, Max-Planck-Institute for Metabolism Research , Notkestrasse 85, 22607 Hamburg, Germany
| | - Rasmus Linser
- Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.,Department Chemistry and Pharmacy, Ludwig-Maximilians-University Munich , Butenandtstrasse 5-13, 81377 Munich, Germany
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21
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Marcos E, Basanta B, Chidyausiku TM, Tang Y, Oberdorfer G, Liu G, Swapna GVT, Guan R, Silva DA, Dou J, Pereira JH, Xiao R, Sankaran B, Zwart PH, Montelione GT, Baker D. Principles for designing proteins with cavities formed by curved β sheets. Science 2017; 355:201-206. [PMID: 28082595 PMCID: PMC5588894 DOI: 10.1126/science.aah7389] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/02/2016] [Indexed: 12/23/2022]
Abstract
Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling β-sheet curvature by studying the geometry of β sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved β sheets topped with α helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that β-sheet curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.
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Affiliation(s)
- Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Benjamin Basanta
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Tamuka M Chidyausiku
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Yuefeng Tang
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Gustav Oberdorfer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria
| | - Gaohua Liu
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - G V T Swapna
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rongjin Guan
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jiayi Dou
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Jose Henrique Pereira
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | | | - Peter H Zwart
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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22
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Colangelo E, Chen Q, Davidson AM, Paramelle D, Sullivan MB, Volk M, Lévy R. Computational and Experimental Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:438-449. [PMID: 27982599 DOI: 10.1021/acs.langmuir.6b04383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The self-assembly and self-organization of small molecules on the surface of nanoparticles constitute a potential route toward the preparation of advanced proteinlike nanosystems. However, their structural characterization, critical to the design of bionanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles (GNPs) is developed using experimentally characterized Cys-Ala-Leu-Asn-Asn (CALNN)- and Cys-Phe-Gly-Ala-Ile-Leu-Ser-Ser (CFGAILSS)-capped GNPs as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated using both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on the peptide capping density and on the nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bionanomaterials.
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Affiliation(s)
- Elena Colangelo
- Institute of Integrative Biology, University of Liverpool , Crown Street, L69 7ZB Liverpool, U.K
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research) , 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632
| | - Qiubo Chen
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632
| | - Adam M Davidson
- Department of Chemistry, University of Liverpool , Liverpool L69 7ZD, U.K
| | - David Paramelle
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research) , 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634
| | - Michael B Sullivan
- Institute of High Performance Computing, A*STAR (Agency for Science, Technology and Research) , 1 Fusionopolis Way, #16-16 Connexis North, Singapore 138632
| | - Martin Volk
- Department of Chemistry, University of Liverpool , Liverpool L69 7ZD, U.K
- Department of Chemistry, Surface Science Research Centre, University of Liverpool , Abercromby Square, Liverpool L69 3BX, U.K
| | - Raphaël Lévy
- Institute of Integrative Biology, University of Liverpool , Crown Street, L69 7ZB Liverpool, U.K
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23
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Ghanavatian P, Khalifeh K, Jafarian V. Structural features and activity of Brazzein and its mutants upon substitution of a surfaced exposed alanine. Biochimie 2016; 131:20-28. [DOI: 10.1016/j.biochi.2016.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 09/06/2016] [Accepted: 09/06/2016] [Indexed: 10/21/2022]
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24
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Abstract
Here, we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs). A TERM is a compact backbone fragment that captures the secondary, tertiary, and quaternary environments around a given residue, comprising one or more disjoint segments (three on average). We seek the set of universal TERMs that capture all structure in the Protein Data Bank (PDB), finding remarkable degeneracy. Only ∼600 TERMs are sufficient to describe 50% of the PDB at sub-Angstrom resolution. However, more rare geometries also exist, and the overall structural coverage grows logarithmically with the number of TERMs. We go on to show that universal TERMs provide an effective mapping between sequence and structure. We demonstrate that TERM-based statistics alone are sufficient to recapitulate close-to-native sequences given either NMR or X-ray backbones. Furthermore, sequence variability predicted from TERM data agrees closely with evolutionary variation. Finally, locations of TERMs in protein chains can be predicted from sequence alone based on sequence signatures emergent from TERM instances in the PDB. For multisegment motifs, this method identifies spatially adjacent fragments that are not contiguous in sequence-a major bottleneck in structure prediction. Although all TERMs recur in diverse proteins, some appear specialized for certain functions, such as interface formation, metal coordination, or even water binding. Structural biology has benefited greatly from previously observed degeneracies in structure. The decomposition of the known structural universe into a finite set of compact TERMs offers exciting opportunities toward better understanding, design, and prediction of protein structure.
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25
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Liu J, Costantino I, Venugopalan N, Fischetti RF, Hyman BT, Frosch MP, Gomez-Isla T, Makowski L. Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue. Sci Rep 2016; 6:33079. [PMID: 27629394 PMCID: PMC5024092 DOI: 10.1038/srep33079] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/15/2016] [Indexed: 12/31/2022] Open
Abstract
Aggregation of Aβ amyloid fibrils into plaques in the brain is a universal hallmark of Alzheimer's Disease (AD), but whether plaques in different individuals are equivalent is unknown. One possibility is that amyloid fibrils exhibit different structures and different structures may contribute differentially to disease, either within an individual brain or between individuals. However, the occurrence and distribution of structural polymorphisms of amyloid in human brain is poorly documented. Here we use X-ray microdiffraction of histological sections of human tissue to map the abundance, orientation and structural heterogeneities of amyloid. Our observations indicate that (i) tissue derived from subjects with different clinical histories may contain different ensembles of fibrillar structures; (ii) plaques harboring distinct amyloid structures can coexist within a single tissue section and (iii) within individual plaques there is a gradient of fibrillar structure from core to margins. These observations have immediate implications for existing theories on the inception and progression of AD.
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Affiliation(s)
- Jiliang Liu
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Isabel Costantino
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Bradley T Hyman
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew P Frosch
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Teresa Gomez-Isla
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, MA, USA
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26
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Lee J, Jang H, Park J, Kim C. Nanotubular self-organization of amide dendrons with focal β-sheet forming peptide units. SOFT MATTER 2016; 12:7453-7456. [PMID: 27714336 DOI: 10.1039/c6sm01408a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To develop rational design principles for a self-organized structure using dendron-peptide conjugates, a β-sheet forming short peptide (VVLL) was introduced to the focal point of a second-generation amide dendron (2G-VVLL) and its self-organization characteristics were investigated. 2G-VVLL self-organized into a nanotubular structure in the aqueous phase. The twisted β-sheet structure of the focal peptide unit was essential for the construction of the nanotubular structure. The design principle could be applied to another dendron-peptide conjugate (2G-AAVV). These findings are expected to assist in the construction of novel precisely controlled nanoarchitectures using amide dendrons with focal peptide units.
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Affiliation(s)
- Jeonghun Lee
- Department of Polymer Science and Engineering, Inha University, 100 Inharo, Nam-gu, Incheon, 22212, Korea.
| | - Hyunil Jang
- Department of Polymer Science and Engineering, Inha University, 100 Inharo, Nam-gu, Incheon, 22212, Korea.
| | - Jonghwan Park
- Department of Polymer Science and Engineering, Inha University, 100 Inharo, Nam-gu, Incheon, 22212, Korea.
| | - Chulhee Kim
- Department of Polymer Science and Engineering, Inha University, 100 Inharo, Nam-gu, Incheon, 22212, Korea.
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27
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The origin of β-strand bending in globular proteins. BMC STRUCTURAL BIOLOGY 2015; 15:21. [PMID: 26492857 PMCID: PMC4618951 DOI: 10.1186/s12900-015-0048-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/06/2015] [Indexed: 11/10/2022]
Abstract
Background Many β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from that for the twist. We, therefore, investigated the physical origin(s) of β-strand bends. Methods We calculated rotation, twist and bend angles for a four-residue short frame. Fixed-length fragments consisting of six residues found in three consecutive short frames were used to evaluate the twist and bend angles of full-length β-strands. Results We calculated and statistically analyzed the twist and bend angles of β-strands found in globular proteins with known three-dimensional structures. The results show that full-length β-strand bend angles are related to the nearby aromatic residue content, whereas local bend angles are related to the nearby aliphatic residue content. Furthermore, it appears that β-strands bend to maximize their hydrophobic contacts with an abutting hydrophobic surface or to form a hydrophobic side-chain cluster when an abutting hydrophobic surface is absent. Conclusions We conclude that the dominant driving force for full-length β-strand bends is the hydrophobic interaction involving aromatic residues, whereas that for local β-strand bends is the hydrophobic interaction involving aliphatic residues. Electronic supplementary material The online version of this article (doi:10.1186/s12900-015-0048-y) contains supplementary material, which is available to authorized users.
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28
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Adhikari B, Bhattacharya D, Cao R, Cheng J. CONFOLD: Residue-residue contact-guided ab initio protein folding. Proteins 2015; 83:1436-49. [PMID: 25974172 PMCID: PMC4509844 DOI: 10.1002/prot.24829] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/11/2015] [Accepted: 05/02/2015] [Indexed: 12/20/2022]
Abstract
Predicted protein residue-residue contacts can be used to build three-dimensional models and consequently to predict protein folds from scratch. A considerable amount of effort is currently being spent to improve contact prediction accuracy, whereas few methods are available to construct protein tertiary structures from predicted contacts. Here, we present an ab initio protein folding method to build three-dimensional models using predicted contacts and secondary structures. Our method first translates contacts and secondary structures into distance, dihedral angle, and hydrogen bond restraints according to a set of new conversion rules, and then provides these restraints as input for a distance geometry algorithm to build tertiary structure models. The initially reconstructed models are used to regenerate a set of physically realistic contact restraints and detect secondary structure patterns, which are then used to reconstruct final structural models. This unique two-stage modeling approach of integrating contacts and secondary structures improves the quality and accuracy of structural models and in particular generates better β-sheets than other algorithms. We validate our method on two standard benchmark datasets using true contacts and secondary structures. Our method improves TM-score of reconstructed protein models by 45% and 42% over the existing method on the two datasets, respectively. On the dataset for benchmarking reconstructions methods with predicted contacts and secondary structures, the average TM-score of best models reconstructed by our method is 0.59, 5.5% higher than the existing method. The CONFOLD web server is available at http://protein.rnet.missouri.edu/confold/.
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Affiliation(s)
- Badri Adhikari
- Department of Computer Science, University of Missouri, Columbia, MO 65211 USA
| | | | - Renzhi Cao
- Department of Computer Science, University of Missouri, Columbia, MO 65211 USA
| | - Jianlin Cheng
- Department of Computer Science, University of Missouri, Columbia, MO 65211 USA
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29
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Affiliation(s)
- Alan C. Gibbs
- Janssen Pharmaceutical Research and Development, LLC, Welsh and McKean Road, Spring House, Pennsylvania 19477-0776, United States
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30
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Jeong WJ, Han S, Park H, Jin KS, Lim YB. Multiplexing Natural Orientation: Oppositely Directed Self-Assembling Peptides. Biomacromolecules 2014; 15:2138-45. [DOI: 10.1021/bm500313f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Woo-jin Jeong
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Sanghun Han
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Hyeseo Park
- Center
for Research Facilities, Yonsei University, Seoul 120-749, Korea
| | - Kyeong Sik Jin
- Pohang
Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Yong-beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
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31
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Joo H, Tsai J. An amino acid code for β-sheet packing structure. Proteins 2014; 82:2128-40. [PMID: 24668690 DOI: 10.1002/prot.24569] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 03/17/2014] [Accepted: 03/19/2014] [Indexed: 11/09/2022]
Abstract
To understand the relationship between protein sequence and structure, this work extends the knob-socket model in an investigation of β-sheet packing. Over a comprehensive set of β-sheet folds, the contacts between residues were used to identify packing cliques: sets of residues that all contact each other. These packing cliques were then classified based on size and contact order. From this analysis, the two types of four-residue packing cliques necessary to describe β-sheet packing were characterized. Both occur between two adjacent hydrogen bonded β-strands. First, defining the secondary structure packing within β-sheets, the combined socket or XY:HG pocket consists of four residues i, i+2 on one strand and j, j+2 on the other. Second, characterizing the tertiary packing between β-sheets, the knob-socket XY:H+B consists of a three-residue XY:H socket (i, i+2 on one strand and j on the other) packed against a knob B residue (residue k distant in sequence). Depending on the packing depth of the knob B residue, two types of knob-sockets are found: side-chain and main-chain sockets. The amino acid composition of the pockets and knob-sockets reveal the sequence specificity of β-sheet packing. For β-sheet formation, the XY:HG pocket clearly shows sequence specificity of amino acids. For tertiary packing, the XY:H+B side-chain and main-chain sockets exhibit distinct amino acid preferences at each position. These relationships define an amino acid code for β-sheet structure and provide an intuitive topological mapping of β-sheet packing.
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Affiliation(s)
- Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, California, 95212
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32
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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33
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Fujiwara K, Ebisawa S, Watanabe Y, Toda H, Ikeguchi M. Local sequence of protein β-strands influences twist and bend angles. Proteins 2014; 82:1484-93. [PMID: 24464770 DOI: 10.1002/prot.24518] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/08/2014] [Accepted: 01/16/2014] [Indexed: 11/08/2022]
Abstract
β-Sheet twisting is thought to be mainly determined by interstrand hydrogen bonds with little contribution from side chains, but some proteins have large, flat β-sheets, suggesting that side chains influence β-structures. We therefore investigated the relationship between amino acid composition and twists or bends of β-strands. We calculated and statistically analyzed the twist and bend angles of short frames of β-strands in known protein structures. The most frequent twist angles were strongly negatively correlated with the proportion of hydrophilic amino acid residues. The majority of hydrophilic residues (except serine and threonine) were found in the edge regions of β-strands, suggesting that the side chains of these residues likely do not affect β-strand structure. In contrast, the majority of serine, threonine, and asparagine side-chains in β-strands made contacts with a nitrogen atom of the main chain, suggesting that these residues suppress β-strand twisting.
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Affiliation(s)
- Kazuo Fujiwara
- Department of Bioinformatics, Soka University, Hachioji, Tokyo, 192-8577, Japan
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34
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Welch WRW, Kubelka J, Keiderling TA. Infrared, vibrational circular dichroism, and Raman spectral simulations for β-sheet structures with various isotopic labels, interstrand, and stacking arrangements using density functional theory. J Phys Chem B 2013; 117:10343-58. [PMID: 23924300 DOI: 10.1021/jp4056126] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infrared (IR), Raman, and vibrational circular dichroism (VCD) spectral variations for different β-sheet structures were studied using simulations based on density functional theory (DFT) force field and intensity computations. The DFT vibrational parameters were obtained for β-sheet fragments containing nine-amides and constrained to a variety of conformations and strand arrangements. These were subsequently transferred onto corresponding larger β-sheet models, normally consisting of five strands with ten amides each, for spectral simulations. Further extension to fibril models composed of multiple stacked β-sheets was achieved by combining the transfer of DFT parameters for each sheet with dipole coupling methods for interactions between sheets. IR spectra of the amide I show different splitting patterns for parallel and antiparallel β-sheets, and their VCD, in the absence of intersheet stacking, have distinct sign variations. Isotopic labeling by (13)C of selected residues yields spectral shifts and intensity changes uniquely sensitive to relative alignment of strands (registry) for antiparallel sheets. Stacking of multiple planar sheets maintains the qualitative spectral character of the single sheet but evidences some reduction in the exciton splitting of the amide I mode. Rotating sheets with respect to each other leads to a significant VCD enhancement, whose sign pattern and intensity is dependent on the handedness and degree of rotation. For twisted β-sheets, a significant VCD enhancement is computed even for sheets stacked with either the same or opposite alignments and the inter-sheet rotation, depending on the sense, can either further increase or weaken the enhanced VCD intensity. In twisted, stacked structures (without rotation), similar VCD amide I patterns (positive couplets) are predicted for both parallel and antiparallel sheets, but different IR intensity distributions still enable their differentiation. Our simulation results prove useful for interpreting experimental vibrational spectra in terms of β-sheet and fibril structure, as illustrated in the accompanying paper.
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Affiliation(s)
- William R W Welch
- Department of Chemistry, University of Wyoming , Laramie, Wyoming 82071, United States
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35
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Guilloux A, Caudron B, Jestin JL. A method to predict edge strands in beta-sheets from protein sequences. Comput Struct Biotechnol J 2013; 7:e201305001. [PMID: 24688737 PMCID: PMC3962219 DOI: 10.5936/csbj.201305001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/27/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022] Open
Abstract
There is a need for rules allowing three-dimensional structure information to be derived from protein sequences. In this work, consideration of an elementary protein folding step allows protein sub-sequences which optimize folding to be derived for any given protein sequence. Classical mechanics applied to this system and the energy conservation law during the elementary folding step yields an equation whose solutions are taken over the field of rational numbers. This formalism is applied to beta-sheets containing two edge strands and at least two central strands. The number of protein sub-sequences optimized for folding per amino acid in beta-strands is shown in particular to predict edge strands from protein sequences. Topological information on beta-strands and loops connecting them is derived for protein sequences with a prediction accuracy of 75%. The statistical significance of the finding is given. Applications in protein structure prediction are envisioned such as for the quality assessment of protein structure models.
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Affiliation(s)
- Antonin Guilloux
- Analyse algébrique, Institut de Mathématiques de Jussieu, Université Pierre et Marie Curie, Paris VI, France
| | - Bernard Caudron
- Centre d'Informatique pour la Biologie, Institut Pasteur, Paris, France
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36
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Valadares NF, Oliveira‐Silva R, Cavini IA, Almeida Marques I, D'Muniz Pereira H, Soares‐Costa A, Henrique‐Silva F, Kalbitzer HR, Munte CE, Garratt RC. X
‐ray crystallography and
NMR
studies of domain‐swapped canecystatin‐1. FEBS J 2013; 280:1028-38. [DOI: 10.1111/febs.12095] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 11/29/2012] [Accepted: 12/03/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Napoleão F. Valadares
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | - Rodrigo Oliveira‐Silva
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | - Italo A. Cavini
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | | | - Humberto D'Muniz Pereira
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | - Andrea Soares‐Costa
- Laboratory of Molecular Biology Department of Genetic and Evolution Federal University of São Carlos Brazil
| | - Flavio Henrique‐Silva
- Laboratory of Molecular Biology Department of Genetic and Evolution Federal University of São Carlos Brazil
| | - Hans R. Kalbitzer
- Institute of Biophysics and Physical Biochemistry University of Regensburg Germany
| | - Claudia E. Munte
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
| | - Richard C. Garratt
- Center for Structural Molecular Biotechnology Department of Physics and Informatics Physics Institute of São Carlos University of São Paulo São Carlos‐SP Brazil
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37
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Caudron B, Jestin J. Sequence criteria for the anti-parallel character of protein beta-strands. J Theor Biol 2012; 315:146-9. [DOI: 10.1016/j.jtbi.2012.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 12/17/2022]
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Abstract
Formation of senile plaques containing amyloid fibrils of Aβ (amyloid β-peptide) is a pathological hallmark of Alzheimer's disease. Unlike globular proteins, which fold into unique structures, the fibrils of Aβ and other amyloid proteins often contain multiple polymorphs. Polymorphism of amyloid fibrils leads to different toxicity in amyloid diseases and may be the basis for prion strains, but the structural origin for fibril polymorphism is still elusive. In the present study we investigate the structural origin of two major fibril polymorphs of Aβ40: an untwisted polymorph formed under agitated conditions and a twisted polymorph formed under quiescent conditions. Using electron paramagnetic resonance spectroscopy, we studied the inter-strand side-chain interactions at 14 spin-labelled positions in the Aβ40 sequence. The results of the present study show that the agitated fibrils have stronger inter-strand spin–spin interactions at most of the residue positions investigated. The two hydrophobic regions at residues 17–20 and 31–36 have the strongest interactions in agitated fibrils. Distance estimates on the basis of the spin exchange frequencies suggest that inter-strand distances at residues 17, 20, 32, 34 and 36 in agitated fibrils are approximately 0.2 Å (1 Å=0.1 nm) closer than in quiescent fibrils. We propose that the strength of inter-strand side-chain interactions determines the degree of β-sheet twist, which then leads to the different association patterns between different cross β-units and thus distinct fibril morphologies. Therefore the inter-strand side-chain interaction may be a structural origin for fibril polymorphism in Aβ and other amyloid proteins.
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39
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Boughton AP, Nguyen K, Andricioaei I, Chen Z. Interfacial orientation and secondary structure change in tachyplesin I: molecular dynamics and sum frequency generation spectroscopy studies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:14343-14351. [PMID: 22054114 PMCID: PMC3235698 DOI: 10.1021/la203192c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent advances in the collection and interpretation of surface-sensitive vibrational spectroscopic measurements have made it possible to study the orientation of peptides and proteins in situ in a biologically relevant environment. However, interpretation of sum frequency generation (SFG) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) vibrational spectroscopy is hindered by the fact that orientation cannot be inferred without some prior knowledge of the protein structure. In this work, molecular dynamics simulations were used to study the interfacial orientation and structural deformation of the short β-sheet peptide tachyplesin I at the polystyrene/water interface. By combining these results with ATR-FTIR and SFG measurements, reasonable agreement was found with the simulation results, suggesting that tachyplesin I lies parallel to the surface, although the simulation results imply a broader distribution of peptide twist angles than could be characterized using available experimental measurements. The interfacial structure was found to be deformable even when disulfide bonds were preserved, and these local deviations from a purely extended β-sheet conformation may be of importance to future developments in the interpretation of SFG and ATR-FTIR spectra.
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Affiliation(s)
- Andrew P. Boughton
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109 USA
| | - Khoi Nguyen
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109 USA
- Department of Applied Chemistry, School of Biotechnology, International University- Vietnam National University, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 70000 Vietnam
| | - Ioan Andricioaei
- Department of Chemistry, University of California at Irvine, 1102 Natural Sciences 2, Irvine, CA 92697 USA
| | - Zhan Chen
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109 USA
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40
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Haworth NL, Feng LL, Wouters MA. HIGH TORSIONAL ENERGY DISULFIDES: RELATIONSHIP BETWEEN CROSS-STRAND DISULFIDES AND RIGHT-HANDED STAPLES. J Bioinform Comput Biol 2011; 4:155-68. [PMID: 16568548 DOI: 10.1142/s0219720006001734] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 08/02/2005] [Accepted: 08/23/2005] [Indexed: 11/18/2022]
Abstract
Redox-active disulfides are capable of being oxidized and reduced under physiological conditions. The enzymatic role of redox-active disulfides in thiol-disulfide reductases is well-known, but redox-active disulfides are also present in non-enzymatic protein structures where they may act as switches of protein function. Here, we examine disulfides linking adjacent β-strands (cross-strand disulfides), which have been reported to be redox-active. Our previous work has established that these cross-strand disulfides have high torsional energies, a quantity likely to be related to the ease with which the disulfide is reduced. We examine the relationship between conformations of disulfides and their location in protein secondary structures. By identifying the overlap between cross-strand disulfides and various conformations, we wish to address whether the high torsional energy of a cross-strand disulfide is sufficient to confer redox activity or whether other factors, such as the presence of the cross-strand disulfide in a strained β-sheet, are required.
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Affiliation(s)
- Naomi L Haworth
- Computational Biology & Bioinformatics Program, Victor Chang Cardiac Research Institute, Level 6, 384 Victoria Rd, Darlinghurst, New South Wales 2010, Australia.
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41
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Murphy BM, Zhang N, Payne RW, Davis JM, Abdul-Fattah AM, Matsuura JE, Herman AC, Manning MC. Structure, stability, and mobility of a lyophilized IgG1 monoclonal antibody as determined using second-derivative infrared spectroscopy. J Pharm Sci 2011; 101:81-91. [PMID: 21918984 DOI: 10.1002/jps.22753] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 06/13/2011] [Accepted: 08/18/2011] [Indexed: 12/11/2022]
Abstract
There are many aspects of stabilization of lyophilized proteins. Of these various factors, retention of native structure, having sufficient amount of stabilizer to embed the protein within an amorphous matrix, and dampening β-relaxations have been shown to be critical in optimizing protein stability during storage. In this study, an IgG1 was lyophilized with varying amounts of sucrose. In some formulations, a small amount of sorbitol was added as a plasticizer. The structure of the protein in dried state was monitored using infrared (IR) spectroscopy. The IR spectra indicated increasing retention of the native structure, which correlated with stability as indicated by size-exclusion chromatography as well as micro-flow imaging. Maximal stability was achieved with a 2:1 mass ratio of sucrose to protein, which is more than that would be expected based on earlier studies. Analysis of both high and low frequency bands associated with intramolecular β-sheet structure provides additional information on the structure of antibodies in the solid state. Finally, there is a correlation between the bandwidth of the β-sheet bands and the enthalpy of relaxation, suggesting that amide I bands can provide some indication of the degree of coupling to the sugar matrix, as well as structural heterogeneity of the protein.
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42
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Affiliation(s)
- Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, México D. F. 09340
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43
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Wigenius J, Andersson MR, Esbjörner EK, Westerlund F. Interactions between a luminescent conjugated polyelectrolyte and amyloid fibrils investigated with flow linear dichroism spectroscopy. Biochem Biophys Res Commun 2011; 408:115-9. [DOI: 10.1016/j.bbrc.2011.03.132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 03/30/2011] [Indexed: 11/28/2022]
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44
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Zhang J, Hao R, Huang L, Yao J, Chen X, Shao Z. Self-assembly of a peptide amphiphile based on hydrolysed Bombyx mori silk fibroin. Chem Commun (Camb) 2011; 47:10296-8. [DOI: 10.1039/c1cc12633d] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Karjalainen EL, Ravi HK, Barth A. Simulation of the amide I absorption of stacked β-sheets. J Phys Chem B 2010; 115:749-57. [PMID: 21174476 DOI: 10.1021/jp109918c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aggregated β-sheet structures are associated with amyloid and prion diseases. Techniques capable of revealing detailed structural and dynamical information on β-sheet structure are thus of great biomedical and biophysical interest. In this work, the infrared (IR) amide I spectral characteristics of stacked β-sheets were modeled using the transition dipole coupling model. For a test set of β-sheet stacks, the simulated amide I spectrum was analyzed with respect to the following parameters; intersheet distance, relative rotation of the sheets with respect to each other and the effect of number of sheets stacked. The amide I maximum shifts about 5 cm(-1) to higher wavenumbers when the intersheet distance between two identical β-sheets decreases from 20 to 5 Å. Rotation around the normal of one of the sheets relative to the other results in maximum intersheet coupling near 0° and 180°. Upon of rotation from 0° to 90° at an intersheet distance of 9 Å, the amide I maximum shifts about 3 cm(-1). Tilting of one of the sheets by 30° from the normal results in a shift of the amide I maximum by less than 1 cm(-1). When stacking several β-sheets along the normal, the amide I maximum shifts to higher wavenumbers with increasing stack size. The amide I maximum shifts about 6 cm(-1) when stacking four sheets with an intersheet distance of 9 Å. The study provides an aid in the interpretation of the IR amide I region for experiments involving β-sheets and creates awareness of the many effects that determine the spectrum of β-sheet structures.
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Affiliation(s)
- Eeva-Liisa Karjalainen
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, SE-106 91, Sweden
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46
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Pashuck ET, Cui H, Stupp SI. Tuning supramolecular rigidity of peptide fibers through molecular structure. J Am Chem Soc 2010; 132:6041-6. [PMID: 20377229 PMCID: PMC2866296 DOI: 10.1021/ja908560n] [Citation(s) in RCA: 311] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We synthesized a series of peptide amphiphiles (PAs) with systematically modified amino acid sequences to control the mechanical properties of the nanofiber gels they form by self-assembly. By manipulating the number and position of valines and alanines in the peptide sequence, we found that valines increase the stiffness of the gel, while additional alanines decrease the mechanical properties. Vitreous ice cryo-transmission electron microscopy shows that all PA molecules investigated here form nanofibers 8-10 nm in diameter and several micrometers in length. We found through Fourier transform IR experiments a strong correlation between gel stiffness and hydrogen bond alignment along the long axis of the fiber. Molecules that form supramolecular structures with the highest mechanical stiffness were found by circular dichroism to self-assemble into beta-sheets with the least amount of twisting and disorder, a result that is consistent with IR experiments. Molecular control of mechanical stiffness in three-dimensional artificial peptide amphiphile matrices offers a chemical strategy to control biological phenomena such as stem cell differentiation and cell morphology.
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Affiliation(s)
- E. Thomas Pashuck
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208
| | - Honggang Cui
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208
| | - Samuel I. Stupp
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
- Department of Medicine, Northwestern University, Evanston, Illinois 60208
- Institute for BioNanotechnology in Medicine Northwestern University, Evanston, Illinois 60208
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47
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Paparcone R, Keten S, Buehler MJ. Atomistic simulation of nanomechanical properties of Alzheimer’s Aβ(1–40) amyloid fibrils under compressive and tensile loading. J Biomech 2010; 43:1196-201. [DOI: 10.1016/j.jbiomech.2009.11.026] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 11/12/2009] [Accepted: 11/22/2009] [Indexed: 11/27/2022]
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48
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Volkova KD, Kovalska VB, Segers-Nolten GM, Veldhuis G, Subramaniam V, Yarmoluk SM. Explorations of the application of cyanine dyes for quantitative α-synuclein detection. Biotech Histochem 2009; 84:55-61. [DOI: 10.1080/10520290902798799] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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49
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Periole X, Rampioni A, Vendruscolo M, Mark AE. Factors That Affect the Degree of Twist in β-Sheet Structures: A Molecular Dynamics Simulation Study of a Cross-β Filament of the GNNQQNY Peptide. J Phys Chem B 2009; 113:1728-37. [DOI: 10.1021/jp8078259] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and School of Molecular and Microbiological Sciences and the Institute of Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Aldo Rampioni
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and School of Molecular and Microbiological Sciences and the Institute of Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Michele Vendruscolo
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and School of Molecular and Microbiological Sciences and the Institute of Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Alan E. Mark
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, and School of Molecular and Microbiological Sciences and the Institute of Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
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50
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Perálvarez-Marín A, Barth A, Gräslund A. Time-resolved infrared spectroscopy of pH-induced aggregation of the Alzheimer Abeta(1-28) peptide. J Mol Biol 2008; 379:589-96. [PMID: 18462754 DOI: 10.1016/j.jmb.2008.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 03/10/2008] [Accepted: 04/06/2008] [Indexed: 10/22/2022]
Abstract
Aggregation of the Alzheimer's disease-related Abeta(1-28) peptide was induced by a rapid, sub-millisecond pH jump and monitored by time-resolved infrared spectroscopy on the millisecond to second time-scale. The release of protons was induced by the photolysis of a caged compound, 1-(2-nitrophenyl)ethyl sulfate (NPE-sulfate). The pH jump generated in our experimental setup is used to model the Abeta peptide structural conversions that may occur in the acidic endosomal/lysosomal cell compartment system. The aggregation of the Abeta(1-28) peptide induced by the pH jump from 8.5 to <6 yields an antiparallel beta-sheet structure. The kinetics of the structural transition is biphasic, showing an initial rapid phase with a transition from random coil to an oligomeric beta-sheet form with a time constant of 3.6 s. This phase is followed by a second slower transition, which yields larger aggregates during 48.0 s.
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Affiliation(s)
- Alex Perálvarez-Marín
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden.
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