1
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Bhagavatula H, Sarkar A, Santra B, Das A. Scan-Find-Scan-Model: Discrete Site-Targeted Suppressor Design Strategy for Amyloid-β. ACS Chem Neurosci 2022; 13:2191-2208. [PMID: 35767676 DOI: 10.1021/acschemneuro.2c00272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Alzheimer's disease is undoubtedly the most well-studied neurodegenerative disease. Consequently, the amyloid-β (Aβ) protein ranks at the top in terms of getting attention from the scientific community for structural property-based characterization. Even after decades of extensive research, there is existing volatility in terms of understanding and hence the effective tackling procedures against the disease that arises due to the lack of knowledge of both specific target- and site-specific drugs. Here, we develop a multidimensional approach based on the characterization of the common static-dynamic-thermodynamic trait of the monomeric protein, which efficiently identifies a small target sequence that contains an inherent tendency to misfold and consequently aggregate. The robustness of the identification of the target sequence comes with an abundance of a priori knowledge about the length and sequence of the target and hence guides toward effective designing of the target-specific drug with a very low probability of bottleneck and failure. Based on the target sequence information, we further identified a specific mutant that showed the maximum potential to act as a destabilizer of the monomeric protein as well as enormous success as an aggregation suppressor. We eventually tested the drug efficacy by estimating the extent of modulation of binding affinity existing within the fibrillar form of the Aβ protein due to a single-point mutation and hence provided a proof of concept of the entire protocol.
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Affiliation(s)
- Hasathi Bhagavatula
- Department of Biotechnology, Progressive Education Society's Modern College of Arts Science and Commerce, Shivajinagar, Pune 411005, India
| | - Archishman Sarkar
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja Subodh Chandra Mallick Road, Kolkata, West Bengal 700032, India
| | - Binit Santra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kalyanpur, Kanpur, Uttar Pradesh 208016, India
| | - Atanu Das
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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2
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Zabrodskaya YA, Shvetsov AV, Garmay YP, Lebedev DV, Dattani R, Egorov VV. Supramolecular Complexes of Tetrapeptides Capable of Inducing the Human α-Lactalbumin β-Domain Conformational Transitions. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Kawasaki T, Yamaguchi Y, Ueda T, Ishikawa Y, Yaji T, Ohta T, Tsukiyama K, Idehara T, Saiki M, Tani M. Irradiation effect of a submillimeter wave from 420 GHz gyrotron on amyloid peptides in vitro. BIOMEDICAL OPTICS EXPRESS 2020; 11:5341-5351. [PMID: 33014618 PMCID: PMC7510884 DOI: 10.1364/boe.395218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
On using the far-infrared radiation system, whether the irradiation effect is thermal or non-thermal is controversial. We irradiated amyloid peptides that are causal factors for amyloidosis by using a submillimeter wave from 420 GHz gyrotron. Fluorescence reagent assay, optical and electron microscopies, and synchrotron-radiation infrared microscopy showed that the irradiation increased the fibrous conformation of peptides at room temperature for 30 min. The temperature increase on the sample was only below 5 K, and a simple heating up to 318 K hardly induced the fibril formation. Therefore, the amyloid aggregation was driven by the far-infrared radiation with little thermal effect.
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Affiliation(s)
- Takayasu Kawasaki
- IR-FEL Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yuusuke Yamaguchi
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Tomomi Ueda
- Department of Applied Chemistry, Faculty of Engineering, Sanyo-Onoda City University, 1-1-1 Daigakudori, Sanyo-Onoda, Yamaguchi 756-0884, Japan
| | - Yuya Ishikawa
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Toyonari Yaji
- SR Center, Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higasi, Kusatsu, Shiga 525-8577, Japan
| | - Toshiaki Ohta
- SR Center, Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higasi, Kusatsu, Shiga 525-8577, Japan
| | - Koichi Tsukiyama
- IR-FEL Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Toshitaka Idehara
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Masatoshi Saiki
- Department of Applied Chemistry, Faculty of Engineering, Sanyo-Onoda City University, 1-1-1 Daigakudori, Sanyo-Onoda, Yamaguchi 756-0884, Japan
| | - Masahiko Tani
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
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4
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Zepeda-Cervantes J, Vaca L. Induction of adaptive immune response by self-aggregating peptides. Expert Rev Vaccines 2018; 17:723-738. [PMID: 30074424 DOI: 10.1080/14760584.2018.1507742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Recently, subunit vaccines are replacing some of the traditional vaccines because they offer a higher margin of safety. However, generally subunit vaccines have low antigenicity. Adjuvants are used in vaccine formulations to increase their immunogenicity, but current research suggests that adjuvants could induce serious side effects in susceptible individuals; therefore, the improvement of antigens and adjuvants is important. AREAS COVERED Here we reviewed some self-aggregating peptides (SAPs) used as antigen delivery systems. SAPs are based on a short sequence of amino acids, which have self-aggregating properties, inducing self-interaction among peptide molecules by means of non-covalent interactions to generate nanoparticles (NPs). EXPERT COMMENTARY SAPs increase the immunogenicity of fused/conjugated antigens because they can interact with antigen-presenting cells and induce adaptive immunity based on both humoral and cellular responses. As an example, we report an antigen delivery system based on SAPs forming NPs. These NPs are synthesized using a recombinant baculovirus. We fused the green fluorescent protein to the first 110 amino acids of polyhedrin protein from Autographa californica nucleopolyhedrovirus, which has self-aggregating properties. We showed that these NPs prompt high antibody levels without inducing inflammation, similarly to some SAPs reported here.
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Affiliation(s)
- Jesus Zepeda-Cervantes
- a Instituto de Fisiología Celular , Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX , Coyoacán , Mexico
| | - Luis Vaca
- a Instituto de Fisiología Celular , Universidad Nacional Autónoma de México, Ciudad Universitaria, CDMX , Coyoacán , Mexico
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5
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Lomont JP, Ostrander JS, Ho JJ, Petti MK, Zanni MT. Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy. J Phys Chem B 2017; 121:8935-8945. [PMID: 28851219 DOI: 10.1021/acs.jpcb.7b06826] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the transition dipole strengths and frequencies of the amyloid β-sheet amide I mode for the aggregated proteins amyloid-β1-40, calcitonin, α-synuclein, and glucagon. According to standard vibrational coupling models for proteins, the frequencies of canonical β-sheets are set by their size and structural and environmental disorder, which determines the delocalization length of the vibrational excitons. The larger the delocalization the lower the frequency of the main infrared-allowed transition, A⊥. The models also predict an accompanying increase in transition dipole strength. For the proteins measured here, we find no correlation between transition dipole strengths and amyloid β-sheet transition frequency. To understand this observation, we have extracted from the protein data bank crystal structures of amyloid peptides from which we calculate the amide I vibrational couplings, and we use these in a model β-sheet Hamiltonian to simulate amyloid vibrational spectra. We find that the variations in amyloid β-sheet structures (e.g., dihedral angles, interstrand distances, and orientations) create significant differences in the average values for interstrand and nearest neighbor couplings, and that those variations encompass the variation in measured A⊥ frequencies. We also find that off-diagonal disorder about the average values explains the range of transition dipole strengths observed experimentally. Thus, we conclude that the lack of correlation between transition dipole-strength and frequency is caused by variations in amyloid β-sheet structure. Taken together, these results indicate that the amide I frequency is very sensitive to amyloid β-sheet structure, the β-sheets of these 4 proteins are not identical, and the assumption that frequency of amyloids scales with β-sheet size cannot be adopted without an accompanying measurement of transition dipole strengths.
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Affiliation(s)
- Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Jia-Jung Ho
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
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6
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Smith DJ, Shell MS. Can Simple Interaction Models Explain Sequence-Dependent Effects in Peptide Homodimerization? J Phys Chem B 2017; 121:5928-5943. [PMID: 28537734 DOI: 10.1021/acs.jpcb.7b03186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The development of rapid methods to explain and predict peptide interactions, aggregation, and self-assembly has become important to understanding amyloid disease pathology, the shelf stability of peptide therapeutics, and the design of novel peptide materials. Although experimental aggregation databases have been used to develop correlative and statistical models, molecular simulations offer atomic-level details that potentially provide greater physical insight and allow one to single out the most explanatory simple models. Here, we outline one such approach using a case study that develops homodimerization models for serine-glycine peptides with various hydrophobic leucine mutations. Using detailed all-atom simulations, we calculate reference dimerization free energy profiles and binding constants for a small peptide library. We then use statistical methods to systematically assess whether simple interaction models, which do not require expensive simulations and free energy calculation, can capture them. Surprisingly, some combinations of a few simple scaling laws well recapitulate the detailed, all-atom results with high accuracy. Specifically, we find that a recently proposed phenomenological hydrophobic force law and coarse measures of entropic effects in binding offer particularly high explanatory power, underscoring the physical relevance to association that these driving forces can play.
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Affiliation(s)
- David J Smith
- Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
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7
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Rigoldi F, Metrangolo P, Redaelli A, Gautieri A. Nanostructure and stability of calcitonin amyloids. J Biol Chem 2017; 292:7348-7357. [PMID: 28283568 PMCID: PMC5418037 DOI: 10.1074/jbc.m116.770271] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/24/2017] [Indexed: 12/03/2022] Open
Abstract
Calcitonin is a 32-amino acid thyroid hormone that can form amyloid fibrils. The structural basis of the fibril formation and stabilization is still debated and poorly understood. The reason is that NMR data strongly suggest antiparallel β-sheet calcitonin assembly, whereas modeling studies on the short DFNKF peptide (corresponding to the sequence from Asp15 to Phe19 of human calcitonin and reported as the minimal amyloidogenic module) show that it assembles with parallel β-sheets. In this work, we first predict the structure of human calcitonin through two complementary molecular dynamics (MD) methods, finding that human calcitonin forms an α-helix. We use extensive MD simulations to compare previously proposed calcitonin fibril structures. We find that two conformations, the parallel arrangement and one of the possible antiparallel structures (with Asp15 and Phe19 aligned), are highly stable and ordered. Nonetheless, fibrils with parallel molecules show bulky loops formed by residues 1 to 7 located on the same side, which could limit or prevent the formation of larger amyloids. We investigate fibrils formed by the DFNKF peptide by simulating different arrangements of this amyloidogenic core sequence. We show that DFNKF fibrils are highly stable when assembled in parallel β-sheets, whereas they quickly unfold in antiparallel conformation. Our results indicate that the DFNKF peptide represents only partially the full-length calcitonin behavior. Contrary to the full-length polypeptide, in fact, the DFNKF sequence is not stable in antiparallel conformation, suggesting that the residue flanking the amyloidogenic peptide contributes to the stabilization of the experimentally observed antiparallel β-sheet packing.
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Affiliation(s)
- Federica Rigoldi
- From the Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Pierangelo Metrangolo
- the Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta," Politecnico di Milano, Via L. Mancinelli 7, 20131 Milano, Italy, and.,the VTT - Tecnical Research Centre of Finland, Biologinkuja 7, 02150 Espoo, Finland
| | - Alberto Redaelli
- From the Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Alfonso Gautieri
- From the Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy,
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8
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Bertolani A, Pizzi A, Pirrie L, Gazzera L, Morra G, Meli M, Colombo G, Genoni A, Cavallo G, Terraneo G, Metrangolo P. Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines. Chemistry 2017; 23:2051-2058. [PMID: 27806188 PMCID: PMC5573999 DOI: 10.1002/chem.201604639] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 12/24/2022]
Abstract
Although intensively studied, the high-resolution crystal structure of the peptide DFNKF, the core-segment of human calcitonin, has never been described. Here we report how the use of iodination as a strategy to promote crystallisation and facilitate phase determination, allowed us to solve, for the first time, the single-crystal X-ray structure of a DFNKF derivative. Computational studies suggest that both the iodinated and the wild-type peptides populate very similar conformations. Furthermore, the conformer found in the solid-state structure is one of the most populated in solution, making the crystal structure a reliable model for the peptide in solution. The crystal structure of DFNKF(I) confirms the overall features of the amyloid cross-β spine and highlights how aromatic-aromatic interactions are important structural factors in the self-assembly of this peptide. A detailed analysis of such interactions is reported.
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Affiliation(s)
- Arianna Bertolani
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Andrea Pizzi
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Lisa Pirrie
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Lara Gazzera
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Giulia Morra
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Massimiliano Meli
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Alessandro Genoni
- Laboratoire SRSMC, UMR 7565CNRSVandoeuvre-lès-Nancy54506France
- Laboratoire SRSMC, UMR 7565Université de LorraineVandoeuvre-lès-Nancy54506France
| | - Gabriella Cavallo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Giancarlo Terraneo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Pierangelo Metrangolo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
- HYBER Centre of ExcellenceDepartment of Applied PhysicsAalto University, P.O. Box 1510002150EspooFinland
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9
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Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
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10
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Zou Y, Sun Y, Zhu Y, Ma B, Nussinov R, Zhang Q. Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein. ACS Chem Neurosci 2016; 7:286-96. [PMID: 26815332 PMCID: PMC7842942 DOI: 10.1021/acschemneuro.5b00242] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aggregation of the copper-zinc superoxide dismutase (SOD1) protein is linked to familial amyotrophic lateral sclerosis, a progressive neurodegenerative disease. A recent experimental study has shown that the (147)GVIGIAQ(153) SOD1 C-terminal segment not only forms amyloid fibrils in isolation but also accelerates the aggregation of full-length SOD1, while substitution of isoleucine at site 149 by proline blocks its fibril formation. Amyloid formation is a nucleation-polymerization process. In this study, we investigated the oligomerization and the nucleus structure of this heptapeptide. By performing extensive replica-exchange molecular dynamics (REMD) simulations and conventional MD simulations, we found that the GVIGIAQ hexamers can adopt highly ordered bilayer β-sheets and β-barrels. In contrast, substitution of I149 by proline significantly reduces the β-sheet probability and results in the disappearance of bilayer β-sheet structures and the increase of disordered hexamers. We identified mixed parallel-antiparallel bilayer β-sheets in both REMD and conventional MD simulations and provided the conformational transition from the experimentally observed parallel bilayer sheets to the mixed parallel-antiparallel bilayer β-sheets. Our simulations suggest that the critical nucleus consists of six peptide chains and two additional peptide chains strongly stabilize this critical nucleus. The stabilized octamer is able to recruit additional random peptides into the β-sheet. Therefore, our simulations provide insights into the critical nucleus formation and the smallest stable nucleus of the (147)GVIGIAQ(153) peptide.
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Affiliation(s)
- Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
| | - Yunxiang Sun
- Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Yuzhen Zhu
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, 399 Chang Hai Road, Shanghai 200438, China
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11
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Fichman G, Guterman T, Adler-Abramovich L, Gazit E. The Use of the Calcitonin Minimal Recognition Module for the Design of DOPA-Containing Fibrillar Assemblies. NANOMATERIALS 2014; 4:726-740. [PMID: 28344244 PMCID: PMC5304689 DOI: 10.3390/nano4030726] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/28/2014] [Accepted: 08/08/2014] [Indexed: 11/20/2022]
Abstract
Amyloid deposits are insoluble fibrous protein aggregates, identified in numerous diseases, which self-assemble through molecular recognition. This process is facilitated by short amino acid sequences, identified as minimal modules. Peptides corresponding to these motifs can be used for the formation of amyloid-like fibrillar assemblies in vitro. Such assemblies hold broad appeal in nanobiotechnology due to their ordered structure and to their ability to be functionalized. The catechol functional group, present in the non-coded L-3,4-dihydroxyphenylalanine (DOPA) amino acid, can take part in diverse chemical interactions. Moreover, DOPA-incorporated polymers have demonstrated adhesive properties and redox activity. In this work, amyloid-like fibrillar assemblies were formed through the self-assembly of a pentapeptide containing DOPA residues, Asp-DOPA-Asn-Lys-DOPA. The design of this peptide was based on the minimal amyloidogenic recognition motif of the human calcitonin hormone, Asp-Phe-Asn-Lys-Phe, the first amyloidogenic pentapeptide identified. By substituting phenylalanine with DOPA, we obtained DOPA-functionalized amyloid-like assemblies in water. Electron microscopy revealed elongated, linear fibril-like nanometric assemblies. Secondary structure analysis indicated the presence of amyloid-characteristic β-sheet structures as well as random coil structures. Deposition of silver on the DOPA-incorporated assemblies suggested redox activity and demonstrated the applicative potential of this novel nanobiomaterial.
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Affiliation(s)
- Galit Fichman
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Tom Guterman
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Lihi Adler-Abramovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel.
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12
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Saini A, Chauhan VS. Self-assembling properties of peptides derived from TDP-43 C-terminal fragment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:3845-3856. [PMID: 24559403 DOI: 10.1021/la404710w] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Two highly fibrillogenic peptide sequences (MNFGAFSINP and EDLIIKGISV) were previously reported in the C-terminal fragment (CTF) of TDP-43 (220-414), a protein recently implicated in neuro-degenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD-U). It was observed that the sequences MNFGAFS and EDLIIKG harbor their respective fibrillogenic domains. Here, the self-assembling properties of peptides obtained by systematic deletion of residues from these two sequences were investigated with the help of light scattering, thioflavin T fluorescence, transmission electron microscopy, and circular dichroism spectroscopy. It was found that the pentapeptide NFGAF and the tetrapeptide DLII are the shortest fibrillogenic sequences from MNFGAFS and EDLIIKG, respectively. Structure function studies revealed that self-assembly of the peptides is largely governed by hydrophobic interactions. Both NFGAF and DLII formed hydrogels based on a complex fibrillar network, at relatively low concentrations, and of remarkable strength and stability. Of particular interest was DLII, a rare aliphatic tetrapeptide that formed a hydrogel at a concentration of 1 mg/mL in less than an hour. Interestingly, various other tetrapeptides based on DLII (YLII, KLII, NLII, and LIID) also formed hydrogels of comparable physical properties, suggesting that an amphipathic peptide design based on the hydrophobic LII motif and a single residue polar terminus is highly favorable for hydrogelation. Peptides discovered in this study, especially DLII and its variants, are some of the shortest ever reported to show such structural and functional features, suggesting that they can be useful templates for the design of peptide-based soft materials.
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Affiliation(s)
- Akash Saini
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Molecular Dynamics Studies on Amyloidogenic Proteins. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [DOI: 10.1007/978-3-642-28554-7_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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Lapidus D, Duka V, Stonkus V, Czaplewski C, Liwo A, Ventura S, Liepina I. Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides. Biopolymers 2012. [DOI: 10.1002/bip.22161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Charge effects on the fibril-forming peptide KTVIIE: a two-dimensional replica exchange simulation study. Biophys J 2012; 102:1952-60. [PMID: 22768952 DOI: 10.1016/j.bpj.2012.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/28/2012] [Accepted: 03/02/2012] [Indexed: 12/12/2022] Open
Abstract
The assembly of peptides into ordered nanostructures is increasingly recognized as both a bioengineering tool for generating new materials and a critical aspect of aggregation processes that underlie neurological diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. There is a major problem in understanding how extremely subtle sequence changes can lead to profound and often unexpected differences in self-assembly behavior. To better delineate the complex interplay of different microscopic driving forces in such cases, we develop a methodology to quantify and compare the propensity of different peptide sequences to form small oligomers during early self-assembly stages. This umbrella-sampling replica exchange molecular dynamics method performs a replica exchange molecular dynamics simulation along peptide association reaction coordinates using umbrella restraints. With this method, we study a set of sequence-similar peptides that differ in net charge: K(+)TVIIE(-), K(+)TVIIE, and (+)K(+)TVIIE. Interestingly, experiments show that only the monovalent peptide, K(+)TVIIE, forms fibrils, whereas the others do not. We examine dimer, trimer, and tetramer formation processes of these peptides, and compute high-accuracy potential of mean force association curves. The potential of mean forces recapitulate a higher stability and equilibrium constant of the fibril-forming peptide, similar to experiment, but reveal that entropic contributions to association free energies can play a surprisingly significant role. The simulations also show behavior reminiscent of experimental aggregate polymorphism, revealed in multiple stable conformational states and association pathways. Our results suggest that sequence changes can have significant effects on self-assembly through not only direct peptide-peptide interactions but conformational entropies and degeneracies as well.
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Invernizzi G, Papaleo E, Sabate R, Ventura S. Protein aggregation: mechanisms and functional consequences. Int J Biochem Cell Biol 2012; 44:1541-54. [PMID: 22713792 DOI: 10.1016/j.biocel.2012.05.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/09/2012] [Accepted: 05/27/2012] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms underlying protein misfolding and aggregation has become a central issue in biology and medicine. Compelling evidence show that the formation of amyloid aggregates has a negative impact in cell function and is behind the most prevalent human degenerative disorders, including Alzheimer's Parkinson's and Huntington's diseases or type 2 diabetes. Surprisingly, the same type of macromolecular assembly is used for specialized functions by different organisms, from bacteria to human. Here we address the conformational properties of these aggregates, their formation pathways, their role in human diseases, their functional properties and how bioinformatics tools might be of help to study these protein assemblies.
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Affiliation(s)
- Gaetano Invernizzi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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17
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Danilkovich AV, Lipkin VM, Udovichenko IP. Classification of self-organizing peptides. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:780-5. [DOI: 10.1134/s1068162011060069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Saini A, Chauhan VS. Delineation of the core aggregation sequences of TDP-43 C-terminal fragment. Chembiochem 2011; 12:2495-501. [PMID: 21905193 DOI: 10.1002/cbic.201100427] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Indexed: 12/12/2022]
Abstract
Ubiquitinated cytoplasmic inclusions of TDP-43 and its C-terminal cleavage products are the pathological hallmarks of amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitinated inclusions. The C-terminal fragments (CTFs) of TDP-43 are increasingly considered to play an important role in its aggregation and in disease. Here, we employed a set of synthetic peptides spanning the length of the TDP-43 CTF (220-414) in order to find out its core aggregation domains. Two regions, one in the RRM-2 domain (246-255) and the other in the C-terminal domain (311-320) of TDP-43, stand out as highly aggregation prone. Studies done on recombinant purified TDP-43 CTF and its three mutants, in which these sequences were deleted individually and together, suggested that the 311-320 region has a more crucial role to play than the 246-255 in its aggregation. The study helps in defining specific peptide sequences that might form the core of TDP-43 aggregation. Identification of these sequences could help in designing peptide based inhibitors of TDP-43 aggregation.
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Affiliation(s)
- Akash Saini
- Malaria Research Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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19
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Maltsev AV, Bystryak S, Galzitskaya OV. The role of β-amyloid peptide in neurodegenerative diseases. Ageing Res Rev 2011; 10:440-52. [PMID: 21406255 DOI: 10.1016/j.arr.2011.03.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 03/03/2011] [Accepted: 03/07/2011] [Indexed: 12/27/2022]
Abstract
Studies of neurodegenerative disorders (NDDs) are drawing more attention of researchers worldwide due to the high incidence of Alzheimer's disease (AD). The pathophysiology of such disorders is, in part, characterized by the transition of a wild-type peptide from its native conformation into a very stable pathological isoform. Subsequently, these abnormal proteins form aggregates of amyloid fibrils that continuously increase in size. Changes in the metabolic processes of neurons (e.g. oxidative stress, hyperphosphorylation of the tau protein, and resulting secondary changes in the cell metabolism) ultimately lead to cell death. We hypothesize that extracellular deposition of β-amyloid peptide fibrils and neurofibrillary tangles represents the body's adaptation mechanism, aimed at preservation of autonomic functioning; while the cognitive decline is severe, the rest of the organ systems remain unaffected and continue to function. This hypothesis is supported by the fact that destruction of pathological plaques, fibrils, and tangles and the use of vaccines targeting β-amyloid result in undesirable side effects. To gain a better understanding of the pathophysiology of Alzheimer's disease and to develop novel therapies, continued studies of the sporadic form of disease and the mechanisms triggering conformational changes in β-amyloid peptide fragments are essential. This review is focused on studies investigating the formation of amyloid fibrils and their role in the pathogenesis of neurodegenerative diseases. In addition, we discuss a related disorder--amyloidosis--where formation of fibrils, tangles, and plaques leads to neuronal death which may occur as a result of a failed adaptation process. Further in-depth investigation and comprehensive analysis of alterations in the metabolism of APP, β-amyloid, and tau protein, which have a pathological effect on cell membrane, alter phosphate exchange, and impair other key metabolic functions of the cell long before the characteristic amyloid deposition takes place, is warranted. A better understanding of intraneuronal processes is crucial in identifying specific inhibitors of pathologic neuronal processes and, consequently, will allow for targeted therapy, thus maximizing efficacy of selected therapeutic regimens.
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Affiliation(s)
- A V Maltsev
- Russian Gerontological Research Clinical Center, Russian Ministry of Health Care, Moscow, Russia.
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20
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Lin YF, Zhao JH, Liu HL, Wu JW, Chuang CK, Liu KT, Lin HY, Tsai WB, Ho Y. Insights into the structural stability and possible aggregation pathways of the LYQLEN peptides derived from human insulin. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Zhao JH, Liu HL, Chuang CK, Liu KT, Tsai WB, Ho Y. Molecular dynamics simulations to investigate the stability and aggregation behaviour of the amyloid-forming peptide VQIVYK from tau protein. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927022.2010.499147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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22
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Abstract
We extend PRIME, an intermediate-resolution protein model previously used in simulations of the aggregation of polyalanine and polyglutamine, to the description of the geometry and energetics of peptides containing all 20 amino acid residues. The 20 amino acid side chains are classified into 14 groups according to their hydrophobicity, polarity, size, charge, and potential for side chain hydrogen bonding. The parameters for extended PRIME, called PRIME 20, include hydrogen-bonding energies, side chain interaction range and energy, and excluded volume. The parameters are obtained by applying a perceptron-learning algorithm and a modified stochastic learning algorithm that optimizes the energy gap between 711 known native states from the PDB and decoy structures generated by gapless threading. The number of independent pair interaction parameters is chosen to be small enough to be physically meaningful yet large enough to give reasonably accurate results in discriminating decoys from native structures. The most physically meaningful results are obtained with 19 energy parameters.
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Affiliation(s)
- Mookyung Cheon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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23
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Shtainfeld A, Sheynis T, Jelinek R. Specific Mutations Alter Fibrillation Kinetics, Fiber Morphologies, and Membrane Interactions of Pentapeptides Derived from Human Calcitonin. Biochemistry 2010; 49:5299-307. [DOI: 10.1021/bi1002713] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Amit Shtainfeld
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Tania Sheynis
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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24
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Abstract
Numerous short peptides have been shown to form beta-sheet amyloid aggregates in vitro. Proteins that contain such sequences are likely to be problematic for a cell, due to their potential to aggregate into toxic structures. We investigated the structures of 30 proteins containing 45 sequences known to form amyloid, to see how the proteins cope with the presence of these potentially toxic sequences, studying secondary structure, hydrogen-bonding, solvent accessible surface area and hydrophobicity. We identified two mechanisms by which proteins avoid aggregation: Firstly, amyloidogenic sequences are often found within helices, despite their inherent preference to form beta structure. Helices may offer a selective advantage, since in order to form amyloid the sequence will presumably have to first unfold and then refold into a beta structure. Secondly, amyloidogenic sequences that are found in beta structure are usually buried within the protein. Surface exposed amyloidogenic sequences are not tolerated in strands, presumably because they lead to protein aggregation via assembly of the amyloidogenic regions. The use of alpha-helices, where amyloidogenic sequences are forced into helix, despite their intrinsic preference for beta structure, is thus a widespread mechanism to avoid protein aggregation.
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Affiliation(s)
- Susan Tzotzos
- Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, United Kingdom
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25
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Tsai HHG, Lee JB, Tseng SS, Pan XA, Shih YC. Folding and membrane insertion of amyloid-beta (25-35) peptide and its mutants: Implications for aggregation and neurotoxicity. Proteins 2010; 78:1909-25. [DOI: 10.1002/prot.22705] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Liu X, Zhao YP. Switch region for pathogenic structural change in conformational disease and its prediction. PLoS One 2010; 5:e8441. [PMID: 20111584 PMCID: PMC2801591 DOI: 10.1371/journal.pone.0008441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 11/27/2009] [Indexed: 11/19/2022] Open
Abstract
Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.
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Affiliation(s)
- Xin Liu
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Ya-Pu Zhao
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
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27
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Liu X, Zhao YP. Simulated pathogenic conformational switch regions matched well with the biochemical findings. J Biomed Inform 2009; 43:365-75. [PMID: 20026248 DOI: 10.1016/j.jbi.2009.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 12/11/2009] [Accepted: 12/14/2009] [Indexed: 10/20/2022]
Abstract
Pathogenic conformational conversion is a general causation of many disease, such as transmissible spongiform encephalopathy (TSE) caused by misfolding of prion, sickle cell anemia, and etc. In such structural changes, misfolding occurs in regions important for the stability of native structure firstly. This destabilizes the normal conformation and leads to subsequent errors in folding pathway. Sites involved in the first stage can be deemed switch regions of the protein, and are vital for conformational conversion. Namely it could be a switch of disease at residue level. Here we report an algorithm that can identify such sites computationally with an accuracy of 93%, by calculating the probability of the native structure of a short segment jumping to a mistake one. Knowledge of such switch sites could be used to target clinical therapy, study physiological and pathologic mechanism of protein, and etc.
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Affiliation(s)
- Xin Liu
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.
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28
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29
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Lin YF, Zhao JH, Liu HL, Liu KT, Chen JT, Tsai WB, Ho Y. Structural stability and aggregation behavior of the VEALYL peptide derived from human insulin: A molecular dynamics simulation study. Biopolymers 2009; 94:269-78. [DOI: 10.1002/bip.21322] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Zanuy D, Ballano G, Jiménez AI, Casanovas J, Haspel N, Cativiela C, Curcó D, Nussinov R, Alemán C. Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. J Chem Inf Model 2009; 49:1623-9. [PMID: 19548653 DOI: 10.1021/ci9001487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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31
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Chang LK, Zhao JH, Liu HL, Liu KT, Chen JT, Tsai WB, Ho Y. Molecular Dynamics Simulations to Investigate the Structural Stability and Aggregation Behavior of the GGVVIA Oligomers Derived from Amyloid β Peptide. J Biomol Struct Dyn 2009; 26:731-40. [DOI: 10.1080/07391102.2009.10507285] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Fang PS, Zhao JH, Liu HL, Liu KT, Chen JT, Lin HY, Huang CH, Fang HW. Molecular Dynamics Simulations to Gain Insights into the Stability and Morphologies of K3 Oligomers from β2-microglobulin. J Biomol Struct Dyn 2009; 26:549-59. [DOI: 10.1080/07391102.2009.10507270] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Li DW, Mohanty S, Irbäck A, Huo S. Formation and growth of oligomers: a Monte Carlo study of an amyloid tau fragment. PLoS Comput Biol 2008; 4:e1000238. [PMID: 19057640 PMCID: PMC2583953 DOI: 10.1371/journal.pcbi.1000238] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/23/2008] [Indexed: 12/14/2022] Open
Abstract
Small oligomers formed early in the process of amyloid fibril formation may be the major toxic species in Alzheimer's disease. We investigate the early stages of amyloid aggregation for the tau fragment AcPHF6 (Ac-VQIVYK-NH2) using an implicit solvent all-atom model and extensive Monte Carlo simulations of 12, 24, and 36 chains. A variety of small metastable aggregates form and dissolve until an aggregate of a critical size and conformation arises. However, the stable oligomers, which are β-sheet-rich and feature many hydrophobic contacts, are not always growth-ready. The simulations indicate instead that these supercritical oligomers spend a lengthy period in equilibrium in which considerable reorganization takes place accompanied by exchange of chains with the solution. Growth competence of the stable oligomers correlates with the alignment of the strands in the β-sheets. The larger aggregates seen in our simulations are all composed of two twisted β-sheets, packed against each other with hydrophobic side chains at the sheet–sheet interface. These β-sandwiches show similarities with the proposed steric zipper structure for PHF6 fibrils but have a mixed parallel/antiparallel β-strand organization as opposed to the parallel organization found in experiments on fibrils. Interestingly, we find that the fraction of parallel β-sheet structure increases with aggregate size. We speculate that the reorganization of the β-sheets into parallel ones is an important rate-limiting step in the formation of PHF6 fibrils. It is believed that the self association of certain protein molecules into aggregated structures, known as amyloid fibrils, plays an important role in a variety of human diseases, such as Alzheimer's disease and Parkinson's disease. Although the ability to form such amyloid fibrils is a common property for proteins, the process leading to these fibrils is incompletely understood. The early stages of the process involve small transient heterogeneous structures made of a few protein chains and are especially difficult to characterize. Here we use atomic-level simulations to explore the early part of the aggregation process for a fibril-forming fragment of the protein tau associated with Alzheimer's disease. We find that a multitude of small aggregates, rich in sheetlike structures, form through a nucleation process. Interestingly, a statistically preferred type of aggregate, consisting of two tightly packed sheets, emerges with increasing aggregate size. Growth of these larger aggregates seems to be a slow process that correlates with the emergence of more uniformly ordered sheets. We speculate that reorganization of the protein chains leading to that ordered arrangement is an important bottleneck to amyloid fibril formation for this peptide.
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Affiliation(s)
- Da-Wei Li
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts, United States of America
| | - Sandipan Mohanty
- John von Neumann Institut für Computing, Forschungszentrum Jülich, Jülich, Germany
| | - Anders Irbäck
- Computational Biology and Biological Physics Division, Department of Theoretical Physics, Lund University, Lund, Sweden
- * E-mail: (AI); (SH)
| | - Shuanghong Huo
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts, United States of America
- * E-mail: (AI); (SH)
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34
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Biancalana M, Makabe K, Koide A, Koide S. Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics. J Mol Biol 2008; 383:205-13. [PMID: 18762191 DOI: 10.1016/j.jmb.2008.08.031] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 08/05/2008] [Accepted: 08/14/2008] [Indexed: 10/21/2022]
Abstract
Though beta-rich self-assemblies comprise a major structural class of polypeptides, a detailed understanding of the determinants of their structure and stability is lacking. In particular, the roles of repetitive stretches of side chains running the long axis of these beta-sheets, termed "cross-strand ladders," remain poorly characterized due to the inherently insoluble and heterogeneous nature of self-assemblies. To overcome these experimental challenges, we have established a complementary experimental system termed "peptide self-assembly mimics" (PSAMs). The PSAMs capture a defined number of self-assembly-like peptide repeats within a soluble beta-rich protein, making structural and energetic studies possible. In this work, we investigated the role of cross-strand ladders containing aromatic residues, which are prominent in self-assembling peptides. A combination of solution data and high-resolution crystal structures revealed that a single cross-strand ladder consisting solely of Tyr significantly stabilized, rigidified, and flattened the PSAM beta-sheet. These characteristics would stabilize each beta-sheet layer of a self-assembly and direct sheet conformations compatible with lamination. Our results therefore provide a rationale for the abundance of aromatic amino acids in fibril-forming peptides and establish important roles of cross-strand Tyr ladders in the structure and stability of beta-rich peptide self-assemblies.
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Affiliation(s)
- Matthew Biancalana
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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35
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Jang S, Shin S. Computational study on the structural diversity of amyloid Beta Peptide (abeta(10-35)) oligomers. J Phys Chem B 2008; 112:3479-84. [PMID: 18303879 DOI: 10.1021/jp076450w] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We studied the oligomerization of Alzheimer amyloid beta peptide (Abeta) using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with Abeta(10-35) dimers, trimers, and tetramers. Extensive REMD simulations illustrated several possible oligomer conformations. As the size of the oligomer increased from a dimer to a tetramer, the number of possible configurations was reduced. We identified all the possible conformations for each oligomer and characterized their temperature dependence. It was found that the detailed structures of the oligomers, which may act as folding intermediates, are highly sensitive to the parameters of the simulation environment such as temperature and concentration. Structural diversities of Abeta oligomers suggest multiple pathways of the aggregation process.
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Affiliation(s)
- Soonmin Jang
- School of Chemistry, Seoul National University, Seoul 151-747, Korea
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36
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van Grondelle W, Iglesias CL, Coll E, Artzner F, Paternostre M, Lacombe F, Cardus M, Martinez G, Montes M, Cherif-Cheikh R, Valéry C. Spontaneous fibrillation of the native neuropeptide hormone Somatostatin-14. J Struct Biol 2007; 160:211-23. [PMID: 17911027 DOI: 10.1016/j.jsb.2007.08.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 08/06/2007] [Accepted: 08/13/2007] [Indexed: 12/18/2022]
Abstract
Natural Somatostatin-14 is a small cyclic neuropeptide hormone with broad inhibitory effects on endocrine secretions. Here we show that natural Somatostatin-14 spontaneously self-assembles in water and in 150 mM NaCl into liquid crystalline nanofibrils, which follow characteristic structural features of amyloid fibrils. These non-covalent highly stable structures are based on the Somatostatin native backbone conformation and are formed under non-denaturing conditions. Our results support the hypothesis that self-assembly into amyloid fibrils is a generic property of the polypeptide chain under appropriate conditions. Given recent advances on the mechanisms of biological storage and sorting modes of peptide/protein hormones into secretory granules, we propose that Somatostatin-14 fibrillation could be relevant to the regulated secretion pathway of this neuropeptide hormone. Such a hypothesis is consistent with the emerging concept of the existence of non-disease related but functional amyloids.
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Affiliation(s)
- Wilmar van Grondelle
- Ipsen Pharma, Carrer Laureà Miró 395, Sant Feliu de Llobregat, 08980 Barcelona, Spain
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37
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Zanuy D, Rodríguez-Ropero F, Haspel N, Zheng J, Nussinov R, Aleman C. Stability of tubular structures based on beta-helical proteins: self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences. Biomacromolecules 2007; 8:3135-46. [PMID: 17854222 DOI: 10.1021/bm700561t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this work we used atomistic molecular dynamics simulations to examine different aspects of tubular nanostructures constructed using protein building blocks with a beta-helical conformation. Initially, we considered two different natural protein building blocks, which were extracted from the protein data base, to compare the relative stabilities of the nanotubes obtained made of self-assembled and covalently linked repeats. Results show nanotubes constructed by linking building blocks through covalent bonds are very stable suggesting that the basic principles of polymer physics are valid when the repeating units are made of large fragments of proteins. In contrast, the stability of self-assembled nanostructures strongly depends on the attractive nonbonding interactions associated to building blocks aligned in a complementary manner. On the other hand, we investigated the ability of a conformationally constrained synthetic amino acid to enhance the stability of both self-assembled and polymerized nanotubes when it is used to substitute natural residues. Specifically, we considered 1-aminocyclopentane-1-caboxylic acid, which involves strong stereochemical constraints produced by the cyclopentane side chain. We found that the incorporation of this amino acid within the more flexible regions of the beta-helical building blocks is an excellent strategy to enhance the stability of the nanotubes. Thus, when a single mutation is performed in the loop region of the beta-helix, the bend architecture of the whole loop is stabilized since the conformational mobility is reduced not only at the mutated position but also at the adjacent positions.
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Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, ETS d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona, Spain.
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Legge FS, Treutlein H, Howlett GJ, Yarovsky I. Molecular dynamics simulations of a fibrillogenic peptide derived from apolipoprotein C-II. Biophys Chem 2007; 130:102-13. [PMID: 17825978 DOI: 10.1016/j.bpc.2007.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Revised: 08/03/2007] [Accepted: 08/03/2007] [Indexed: 01/17/2023]
Abstract
The pathway to amyloid fibril formation in proteins involves specific structural changes leading to the combination of misfolded intermediates into oligomeric assemblies. Recent NMR studies showed the presence of "turns" in amyloid peptides, indicating that turn formation may play an important role in the nucleation of the intramolecular folding and possible assembly of amyloid. Fully solvated all-atom molecular dynamics simulations were used to study the structure and dynamics of the apolipoprotein C-II peptide 56 to 76, associated with the formation of amyloid fibrils. The peptide populated an ensemble of turn structures, stabilized by hydrogen bonds and hydrophobic interactions enabling the formation of a strong hydrophobic core which may provide the conditions required to initiate aggregation. Two competing mechanisms discussed in the literature were observed. This has implications in understanding the mechanism of amyloid formation in not only apoC-II and its fragments, but also in other amyloidogenic peptides.
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Affiliation(s)
- F Sue Legge
- Applied Physics, School of Applied Sciences, RMIT University, GPO Box 2476V Melbourne, Victoria, 3001, Australia
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39
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Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R. Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer. Biophys J 2007; 93:245-53. [PMID: 17416628 PMCID: PMC1914416 DOI: 10.1529/biophysj.106.100644] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this work we present a computational approach to the design of nanostructures made of structural motifs taken from left-handed beta-helical proteins. Previously, we suggested a structural model based on the self-assembly of motifs taken from Escherichia coli galactoside acetyltransferase (Protein Data Bank 1krr, chain A, residues 131-165, denoted krr1), which produced a very stable nanotube in molecular dynamics simulations. Here we modify this model by changing the charge distribution in the inner core of the system and testing the effect of this change on the structural arrangement of the construct. Our results demonstrate that it is possible to generate the proper conditions for charge transfer inside nanotubes based on assemblies of krr1 segment. The electronic transfer would be achieved by introducing different histidine ionization states in selected positions of the internal core of the construct, in addition to specific mutations with charged amino acids that altogether will allow the formation of coherent networks of aromatic ring stacking, salt-bridges, and hydrogen bonds.
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Affiliation(s)
- Nurit Haspel
- School of Computer Science Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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40
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Yan S, Gawlak G, Makabe K, Tereshko V, Koide A, Koide S. Hydrophobic surface burial is the major stability determinant of a flat, single-layer beta-sheet. J Mol Biol 2007; 368:230-43. [PMID: 17335845 PMCID: PMC1995161 DOI: 10.1016/j.jmb.2007.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Revised: 01/29/2007] [Accepted: 02/01/2007] [Indexed: 10/23/2022]
Abstract
Formation of a flat beta-sheet is a fundamental event in beta-sheet-mediated protein self-assembly. To investigate the contributions of various factors to the stability of flat beta-sheets, we performed extensive alanine-scanning mutagenesis experiments on the single-layer beta-sheet segment of Borrelia outer surface protein A (OspA). This beta-sheet segment consists of beta-strands with highly regular geometries that can serve as a building block for self-assembly. Our Ala-scanning approach is distinct from the conventional host-guest method, in that it introduces only conservative, truncation mutations that should minimize structural perturbation. Our results showed very weak correlation with experimental beta-sheet propensity scales, statistical beta-sheet propensity scales, or cross-strand pairwise correlations. In contrast, our data showed strong positive correlation with the change in buried non-polar surface area. Polar interactions including prominent Glu-Lys cross-strand pairs contribute marginally to the beta-sheet stability. These results were corroborated by results from additional non-Ala mutations. Taken together, these results demonstrate the dominant contribution of non-polar surface burial to flat beta-sheet stability even at solvent-exposed positions. The OspA single-layer beta-sheet achieves efficient hydrophobic surface burial without forming a hydrophobic core by a strategic placement of a variety of side-chains. These findings further suggest the importance of hydrophobic interactions within a beta-sheet layer in peptide self-assembly.
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Affiliation(s)
- Shude Yan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, U.S.A
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, U.S.A
| | - Grzegorz Gawlak
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, U.S.A
| | - Koki Makabe
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, U.S.A
| | - Valentina Tereshko
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, U.S.A
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, U.S.A
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, U.S.A
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, U.S.A
- *Corresponding author: Shohei Koide Department of Biochemistry and Molecular Biology, The University of Chicago 920 E. 58th Street, Chicago, IL 60637, U.S.A. Fax: 1-773-702-0439 E-mail:
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41
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Levy M, Garmy N, Gazit E, Fantini J. The minimal amyloid-forming fragment of the islet amyloid polypeptide is a glycolipid-binding domain. FEBS J 2007; 273:5724-35. [PMID: 17212787 DOI: 10.1111/j.1742-4658.2006.05562.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several proteins that interact with cell surface glycolipids share a common fold with a solvent-exposed aromatic residue that stacks onto a sugar ring of the glycolipid (CH-pi stacking interaction). Stacking interactions between aromatic residues (pi-pi stacking) also play a pivotal role in the assembly process, including many cases of amyloid fibril formation. We found a structural similarity between a typical glycolipid-binding domain (the V3 loop of HIV-1 gp120) and the minimal amyloid-forming fragment of the human islet amyloid polypeptide, i.e. the octapeptide core module NFGAILSS. In a monolayer assay at the air-water interface, the NFGAILSS peptide specifically interacted with the glycolipid lactosylceramide. The interaction appears to require an aromatic residue, as NLGAILSS was poorly recognized by lactosylceramide, whereas NYGAILSS behaved like NFGAILSS. In addition, we observed that the full-length human islet amyloid polypeptide (1-37) did interact with a monolayer of lactosylceramide, and that the glycolipid film significantly affected the aggregation process of the peptide. As glycolipid-V3 interactions are efficiently inhibited by suramin, a polyaromatic compound, we investigated the effects of suramin on amyloid formation by human islet amyloid polypeptide. We found that suramin inhibited amyloid fibril formation at low concentrations, but dramatically stimulated the process at high concentrations. Taken together, our results indicate that the minimal amyloid-forming fragment of human islet amyloid polypeptide is a glycolipid-binding domain, and provide further experimental support for the role of aromatic pi-pi and CH-pi stacking interactions in the molecular control of the amyloidogenesis process.
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Affiliation(s)
- Michal Levy
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Israel
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42
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Gazit E. Self assembly of short aromatic peptides into amyloid fibrils and related nanostructures. Prion 2007; 1:32-5. [PMID: 19164892 DOI: 10.4161/pri.1.1.4095] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The formation of amyloid fibrils is the hallmark of more than twenty human disorders of unrelated etiology. In all these cases, ordered fibrillar protein assemblies with a diameter of 7-10 nm are being observed. In spite of the great clinical important of amyloid-associated diseases, the molecular recognition and self-assembly processes that lead to the formation of the fibrils are not fully understood. One direction to decipher the mechanism of amyloid formation is the use of short peptides fragments as model systems. Short peptide fragments, as short as pentapeptides, were shown to form typical amyloid assemblies in vitro that have ultrastructural, biophysical, and cytotoxic properties, as those of assemblies that are being formed by full length polypeptides. When we analyzed such short fragments, we identified the central role of aromatic moieties in the ability to aggregate into ordered nano-fibrillar structures. This notion allowed us to discover additional very short amyloidogenic peptides as well as other aromatic peptide motifs, which can form various assemblies at the nano-scale (including nanotubes, nanospheres, and macroscopic hydrogels with nano-scale order). Other practical utilization of this concept, together with novel beta breakage methods, is their use for the development of novel classes of amyloid formation inhibitors.
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Affiliation(s)
- Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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43
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44
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Makabe K, McElheny D, Tereshko V, Hilyard A, Gawlak G, Yan S, Koide A, Koide S. Atomic structures of peptide self-assembly mimics. Proc Natl Acad Sci U S A 2006; 103:17753-8. [PMID: 17093048 PMCID: PMC1693819 DOI: 10.1073/pnas.0606690103] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Indexed: 11/18/2022] Open
Abstract
Although the beta-rich self-assemblies are a major structural class for polypeptides and the focus of intense research, little is known about their atomic structures and dynamics due to their insoluble and noncrystalline nature. We developed a protein engineering strategy that captures a self-assembly segment in a water-soluble molecule. A predefined number of self-assembling peptide units are linked, and the beta-sheet ends are capped to prevent aggregation, which yields a mono-dispersed soluble protein. We tested this strategy by using Borrelia outer surface protein (OspA) whose single-layer beta-sheet located between two globular domains consists of two beta-hairpin units and thus can be considered as a prototype of self-assembly. We constructed self-assembly mimics of different sizes and determined their atomic structures using x-ray crystallography and NMR spectroscopy. Highly regular beta-sheet geometries were maintained in these structures, and peptide units had a nearly identical conformation, supporting the concept that a peptide in the regular beta-geometry is primed for self-assembly. However, we found small but significant differences in the relative orientation between adjacent peptide units in terms of beta-sheet twist and bend, suggesting their inherent flexibility. Modeling shows how this conformational diversity, when propagated over a large number of peptide units, can lead to a substantial degree of nanoscale polymorphism of self-assemblies.
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Affiliation(s)
- Koki Makabe
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Dan McElheny
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Valentia Tereshko
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Aaron Hilyard
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Grzegorz Gawlak
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Shude Yan
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637
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45
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Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. Prediction of amyloidogenic and disordered regions in protein chains. PLoS Comput Biol 2006; 2:e177. [PMID: 17196033 PMCID: PMC1761655 DOI: 10.1371/journal.pcbi.0020177] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Accepted: 11/06/2006] [Indexed: 11/19/2022] Open
Abstract
The determination of factors that influence protein conformational changes is very important for the identification of potentially amyloidogenic and disordered regions in polypeptide chains. In our work we introduce a new parameter, mean packing density, to detect both amyloidogenic and disordered regions in a protein sequence. It has been shown that regions with strong expected packing density are responsible for amyloid formation. Our predictions are consistent with known disease-related amyloidogenic regions for eight of 12 amyloid-forming proteins and peptides in which the positions of amyloidogenic regions have been revealed experimentally. Our findings support the concept that the mechanism of amyloid fibril formation is similar for different peptides and proteins. Moreover, we have demonstrated that regions with weak expected packing density are responsible for the appearance of disordered regions. Our method has been tested on datasets of globular proteins and long disordered protein segments, and it shows improved performance over other widely used methods. Thus, we demonstrate that the expected packing density is a useful value with which one can predict both intrinsically disordered and amyloidogenic regions of a protein based on sequence alone. Our results are important for understanding the structural characteristics of protein folding and misfolding.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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46
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Zheng J, Ma B, Nussinov R. Consensus features in amyloid fibrils: sheet–sheet recognition via a (polar or nonpolar) zipper structure. Phys Biol 2006; 3:P1-4. [PMID: 17021379 DOI: 10.1088/1478-3975/3/3/p01] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Amyloid fibrils characterized as highly intractable thread-like species are associated with many neurodegenerative diseases. Although neither the mechanism of amyloid formation nor the origin of amyloid toxicity is currently completely understood, the detailed three-dimensional atomic structures of the yeast protein Sup35 and Abeta amyloid protein determined by recent experiments provide the first and important step towards the comprehension of the pathogenesis and aggregation mechanisms of amyloid diseases. By analyzing these two amyloid peptides which have available crystal structures and other amyloid sequences with proposed structures using computational simulations, we delineate three common features in amyloid organizations and amyloid structures. These could contribute to an improved understanding of the molecular mechanism of amyloid formation, the nature of the aggregation driving forces that stabilize these structures and the development of potential therapeutic agents against amyloid diseases.
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Affiliation(s)
- Jie Zheng
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
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47
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Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. A search for amyloidogenic regions in protein chains. Mol Biol 2006. [DOI: 10.1134/s0026893306050189] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Melquiond A, Mousseau N, Derreumaux P. Structures of soluble amyloid oligomers from computer simulations. Proteins 2006; 65:180-91. [PMID: 16894607 DOI: 10.1002/prot.21100] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Alzheimer's, Parkinson's, and Creutzfeldt-Jakob's neurodegenerative diseases are all linked with the assembly of normally soluble proteins into amyloid fibrils. Because of experimental limitations, structural characterization of the soluble oligomers, which form early in the process of fibrillogenesis and are cytotoxic, remains to be determined. In this article, we study the aggregation paths of seven chains of the shortest amyloid-forming peptide, using an activitated method and a reduced atomic representation. Our simulations show that disordered KFFE monomers ultimately form three distinct topologies of similar energy: amorphous oligomers, incomplete rings with beta-barrel character, and cross-beta-sheet structures with the meridional but not the equatorial X-ray fiber reflections. The simulations also shed light on the pathways from misfolded aggregates to fibrillar-like structures. They also underline the multiplicity of building blocks that can lead to the formation of the critical nucleus from which rapid growth of the fibril occurs.
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Affiliation(s)
- Adrien Melquiond
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique et Université Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
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49
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Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. Is it possible to predict amyloidogenic regions from sequence alone? J Bioinform Comput Biol 2006; 4:373-88. [PMID: 16819789 DOI: 10.1142/s0219720006002004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2005] [Accepted: 11/02/2005] [Indexed: 11/18/2022]
Abstract
Identification of potentially amyloidogenic regions in polypeptide chains is very important because the amyloid fibril formation can be induced in most normal proteins. In our work we suggest a new method to detect amyloidogenic regions in protein sequence. It is based on the assumption that packing is tight inside an amyloid and therefore regions which could potentially pack well would have a tendency to form amyloids. This means that the regions with strong expected packing of residues would be responsible for the amyloid formation. We use this property to identify potentially amyloidogenic regions in proteins basing on their amino acid sequences only. Our predictions are consistent with known disease-related amyloidogenic regions for 8 of 11 amyloid-forming proteins and peptides in which the positions of amyloidogenic regions have been revealed experimentally. Predictions of the regions which are responsible for the formation of amyloid fibrils in proteins unrelated to disease have been also done.
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya str., 4, Pushchino, Moscow Region, 142290, Russia.
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50
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Röhrig UF, Laio A, Tantalo N, Parrinello M, Petronzio R. Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer. Biophys J 2006; 91:3217-29. [PMID: 16920832 PMCID: PMC1614475 DOI: 10.1529/biophysj.106.088542] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases are associated with amyloid fibrils formed by different polypeptides. We probe the structure and stability of oligomers of different sizes of the fragment Abeta(16-22) of the Alzheimer beta-amyloid peptide using atomic-detail molecular dynamics simulations with explicit solvent. We find that only large oligomers form a stable beta-sheet aggregate, the minimum nucleus size being of the order of 8-16 peptides. This effect is attributed to better hydrophobic contacts and a better shielding of backbone-backbone hydrogen bonds from the solvent in bigger assemblies. Moreover, the observed stability of beta-sheet aggregates with a different number of layers can be explained on the basis of their solvent-accessible surface area. Depending on the stacking interface between the sheets, we observe straight or twisted structures, which could be linked to the experimentally observed polymorphism of amyloid fibrils. To compare our 32-mer structure to experimental data, we calculate its x-ray diffraction pattern. Good agreement is found between experimentally and theoretically determined reflections, suggesting that our model indeed closely resembles the structures found in vitro.
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Affiliation(s)
- Ute F Röhrig
- Centro Studi e Ricerche Enrico Fermi, Compendio Viminale, Rome, Italy.
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